Hugging Face's logo

tintin1027
/
final

Model card Files
xet
 Community
tintin1027 commited on
Commit
2606ba3
·
verified ·
1 Parent(s): ae10e20

Upload folder from local machine

Browse files
Files changed (24) hide show
  1. .gitattributes +7 -0
  2. data/processed/scPerturb/latent_flow_replogle_k562_essential/condition_vocab.json +2059 -0
  3. data/processed/scPerturb/latent_flow_replogle_k562_essential/figure_manifest.txt +12 -0
  4. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/01_split_condition_counts.png +0 -0
  5. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/02_top30_perturbation_gene_counts.png +3 -0
  6. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/03_top_genes_split_composition.png +3 -0
  7. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/04_umi_distribution.png +0 -0
  8. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/05_ngenes_distribution.png +0 -0
  9. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/06_latent_cumulative_explained_variance.png +0 -0
  10. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/07_latent_scatter_by_split.png +3 -0
  11. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/08_latent_scatter_by_condition.png +3 -0
  12. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/09_latent_norm_by_split_condition.png +0 -0
  13. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/10_mean_latent_heatmap_by_split.png +0 -0
  14. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/11_split_gene_count_heatmap_subset.png +3 -0
  15. data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/12_gene_annotation_summary.png +0 -0
  16. data/processed/scPerturb/latent_flow_replogle_k562_essential/flow_indices.pkl +3 -0
  17. data/processed/scPerturb/latent_flow_replogle_k562_essential/flow_tensors.pt +3 -0
  18. data/processed/scPerturb/latent_flow_replogle_k562_essential/latent_decoder.pkl +3 -0
  19. data/processed/scPerturb/latent_flow_replogle_k562_essential/replogle_k562_essential_latent_flow_ready.h5ad +3 -0
  20. data/processed/scPerturb/latent_flow_replogle_k562_essential/summary.csv +19 -0
  21. data/processed/scPerturb/prediction_ready/replogle_k562_essential_prediction_ready_summary_full.csv +12 -0
  22. data/processed/scPerturb/prediction_ready/replogle_k562_essential_single_gene_prediction_ready_full.h5ad +3 -0
  23. src/data/latent_space.ipynb +493 -23
  24. src/data/replogle_k562_essential_scdfm_preprocess.ipynb +0 -0
.gitattributes CHANGED
@@ -56,3 +56,10 @@ data/scPerturb/rna_protein/ReplogleWeissman2022_K562_gwps.h5ad.part filter=lfs d
56
  scDFM/assets/fig1.png filter=lfs diff=lfs merge=lfs -text
57
  scDFM/assets/logo.png filter=lfs diff=lfs merge=lfs -text
58
  scDFM/assets/scdfm_PPT.pdf filter=lfs diff=lfs merge=lfs -text
 
 
 
 
 
 
 
 
56
  scDFM/assets/fig1.png filter=lfs diff=lfs merge=lfs -text
57
  scDFM/assets/logo.png filter=lfs diff=lfs merge=lfs -text
58
  scDFM/assets/scdfm_PPT.pdf filter=lfs diff=lfs merge=lfs -text
59
+ data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/02_top30_perturbation_gene_counts.png filter=lfs diff=lfs merge=lfs -text
60
+ data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/03_top_genes_split_composition.png filter=lfs diff=lfs merge=lfs -text
61
+ data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/07_latent_scatter_by_split.png filter=lfs diff=lfs merge=lfs -text
62
+ data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/08_latent_scatter_by_condition.png filter=lfs diff=lfs merge=lfs -text
63
+ data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/11_split_gene_count_heatmap_subset.png filter=lfs diff=lfs merge=lfs -text
64
+ data/processed/scPerturb/latent_flow_replogle_k562_essential/replogle_k562_essential_latent_flow_ready.h5ad filter=lfs diff=lfs merge=lfs -text
65
+ data/processed/scPerturb/prediction_ready/replogle_k562_essential_single_gene_prediction_ready_full.h5ad filter=lfs diff=lfs merge=lfs -text
data/processed/scPerturb/latent_flow_replogle_k562_essential/condition_vocab.json ADDED
@@ -0,0 +1,2059 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "control": 0,
3
+ "AAAS": 1,
4
+ "AAMP": 2,
5
+ "AARS": 3,
6
+ "AARS2": 4,
7
+ "AASDHPPT": 5,
8
+ "AATF": 6,
9
+ "ABCB10": 7,
10
+ "ABCB7": 8,
11
+ "ABCE1": 9,
12
+ "ABCF1": 10,
13
+ "ABCG1": 11,
14
+ "ABHD11": 12,
15
+ "ABHD17A": 13,
16
+ "ABT1": 14,
17
+ "ACD": 15,
18
+ "ACIN1": 16,
19
+ "ACOT12": 17,
20
+ "ACTB": 18,
21
+ "ACTL6A": 19,
22
+ "ACTR10": 20,
23
+ "ACTR1A": 21,
24
+ "ACTR1B": 22,
25
+ "ACTR2": 23,
26
+ "ACTR3": 24,
27
+ "ACTR6": 25,
28
+ "ACTR8": 26,
29
+ "ADAT2": 27,
30
+ "ADAT3": 28,
31
+ "ADRM1": 29,
32
+ "ADSL": 30,
33
+ "AFG3L2": 31,
34
+ "AHCTF1": 32,
35
+ "AHCY": 33,
36
+ "AIFM1": 34,
37
+ "AKIRIN2": 35,
38
+ "ALDOA": 36,
39
+ "ALG1": 37,
40
+ "ALG11": 38,
41
+ "ALG13": 39,
42
+ "ALG14": 40,
43
+ "ALG1L": 41,
44
+ "ALG2": 42,
45
+ "ALYREF": 43,
46
+ "ANAPC1": 44,
47
+ "ANAPC10": 45,
48
+ "ANAPC11": 46,
49
+ "ANAPC13": 47,
50
+ "ANAPC15": 48,
51
+ "ANAPC2": 49,
52
+ "ANAPC4": 50,
53
+ "ANAPC5": 51,
54
+ "ANKLE2": 52,
55
+ "ANKRD11": 53,
56
+ "ANKRD49": 54,
57
+ "ANKS6": 55,
58
+ "ANLN": 56,
59
+ "AP2M1": 57,
60
+ "AP2S1": 58,
61
+ "AQP7": 59,
62
+ "AQR": 60,
63
+ "ARCN1": 61,
64
+ "ARF4": 62,
65
+ "ARFRP1": 63,
66
+ "ARGFX": 64,
67
+ "ARGLU1": 65,
68
+ "ARHGAP11B": 66,
69
+ "ARID3A": 67,
70
+ "ARIH1": 68,
71
+ "ARL2": 69,
72
+ "ARL4D": 70,
73
+ "ARMC6": 71,
74
+ "ARMC7": 72,
75
+ "ARPC2": 73,
76
+ "ARPC3": 74,
77
+ "ARPC4": 75,
78
+ "ASF1B": 76,
79
+ "ATF4": 77,
80
+ "ATF5": 78,
81
+ "ATL2": 79,
82
+ "ATP1A1": 80,
83
+ "ATP2A2": 81,
84
+ "ATP6AP1": 82,
85
+ "ATP6AP2": 83,
86
+ "ATP6V0B": 84,
87
+ "ATP6V0C": 85,
88
+ "ATP6V0D1": 86,
89
+ "ATP6V1A": 87,
90
+ "ATP6V1B2": 88,
91
+ "ATP6V1C1": 89,
92
+ "ATP6V1D": 90,
93
+ "ATP6V1E1": 91,
94
+ "ATP6V1F": 92,
95
+ "ATP6V1G1": 93,
96
+ "ATP6V1H": 94,
97
+ "ATR": 95,
98
+ "ATRIP": 96,
99
+ "AURKA": 97,
100
+ "AURKAIP1": 98,
101
+ "AURKB": 99,
102
+ "BANF1": 100,
103
+ "BANP": 101,
104
+ "BAP1": 102,
105
+ "BARD1": 103,
106
+ "BCAR1": 104,
107
+ "BCAS2": 105,
108
+ "BCL2L1": 106,
109
+ "BCLAF1": 107,
110
+ "BCR": 108,
111
+ "BCS1L": 109,
112
+ "BDP1": 110,
113
+ "BET1": 111,
114
+ "BGLAP": 112,
115
+ "BIRC5": 113,
116
+ "BMS1": 114,
117
+ "BNIP1": 115,
118
+ "BOP1": 116,
119
+ "BORA": 117,
120
+ "BPTF": 118,
121
+ "BRCA1": 119,
122
+ "BRCA2": 120,
123
+ "BRD4": 121,
124
+ "BRD8": 122,
125
+ "BRF1": 123,
126
+ "BRF2": 124,
127
+ "BRIP1": 125,
128
+ "BRIX1": 126,
129
+ "BRK1": 127,
130
+ "BTF3": 128,
131
+ "BTF3L4": 129,
132
+ "BUB1": 130,
133
+ "BUB1B": 131,
134
+ "BUB3": 132,
135
+ "BUD13": 133,
136
+ "BUD31": 134,
137
+ "BYSL": 135,
138
+ "C12orf45": 136,
139
+ "C12orf60": 137,
140
+ "C14orf178": 138,
141
+ "C16orf86": 139,
142
+ "C17orf58": 140,
143
+ "C19orf25": 141,
144
+ "C19orf53": 142,
145
+ "C1D": 143,
146
+ "C1QBP": 144,
147
+ "C1QTNF4": 145,
148
+ "C1orf109": 146,
149
+ "C6orf15": 147,
150
+ "C7orf26": 148,
151
+ "C7orf50": 149,
152
+ "C9orf16": 150,
153
+ "C9orf78": 151,
154
+ "CA5A": 152,
155
+ "CACNB3": 153,
156
+ "CACTIN": 154,
157
+ "CADM4": 155,
158
+ "CAMLG": 156,
159
+ "CAP1": 157,
160
+ "CAPZB": 158,
161
+ "CARS": 159,
162
+ "CASP8AP2": 160,
163
+ "CBLL1": 161,
164
+ "CBLN1": 162,
165
+ "CBX1": 163,
166
+ "CCAR1": 164,
167
+ "CCDC115": 165,
168
+ "CCDC130": 166,
169
+ "CCDC137": 167,
170
+ "CCDC144A": 168,
171
+ "CCDC144NL": 169,
172
+ "CCDC174": 170,
173
+ "CCDC59": 171,
174
+ "CCDC78": 172,
175
+ "CCDC84": 173,
176
+ "CCDC86": 174,
177
+ "CCNA2": 175,
178
+ "CCNB1": 176,
179
+ "CCND1": 177,
180
+ "CCNH": 178,
181
+ "CCNK": 179,
182
+ "CCNL1": 180,
183
+ "CCP110": 181,
184
+ "CCT2": 182,
185
+ "CCT3": 183,
186
+ "CCT4": 184,
187
+ "CCT5": 185,
188
+ "CCT6A": 186,
189
+ "CCT7": 187,
190
+ "CCT8": 188,
191
+ "CD2BP2": 189,
192
+ "CD3EAP": 190,
193
+ "CD8B": 191,
194
+ "CDAN1": 192,
195
+ "CDC123": 193,
196
+ "CDC16": 194,
197
+ "CDC20": 195,
198
+ "CDC23": 196,
199
+ "CDC26": 197,
200
+ "CDC27": 198,
201
+ "CDC37": 199,
202
+ "CDC40": 200,
203
+ "CDC42": 201,
204
+ "CDC45": 202,
205
+ "CDC5L": 203,
206
+ "CDC6": 204,
207
+ "CDC7": 205,
208
+ "CDC73": 206,
209
+ "CDCA5": 207,
210
+ "CDCA8": 208,
211
+ "CDIPT": 209,
212
+ "CDK1": 210,
213
+ "CDK11A": 211,
214
+ "CDK2": 212,
215
+ "CDK7": 213,
216
+ "CDK9": 214,
217
+ "CDT1": 215,
218
+ "CEBPZ": 216,
219
+ "CENPA": 217,
220
+ "CENPC": 218,
221
+ "CENPE": 219,
222
+ "CENPH": 220,
223
+ "CENPI": 221,
224
+ "CENPJ": 222,
225
+ "CENPK": 223,
226
+ "CENPN": 224,
227
+ "CENPT": 225,
228
+ "CENPW": 226,
229
+ "CEP152": 227,
230
+ "CEP192": 228,
231
+ "CEP68": 229,
232
+ "CEP85": 230,
233
+ "CEP97": 231,
234
+ "CFDP1": 232,
235
+ "CFL1": 233,
236
+ "CHAF1A": 234,
237
+ "CHAF1B": 235,
238
+ "CHCHD1": 236,
239
+ "CHCHD2": 237,
240
+ "CHCHD4": 238,
241
+ "CHD4": 239,
242
+ "CHEK1": 240,
243
+ "CHERP": 241,
244
+ "CHMP1A": 242,
245
+ "CHMP2A": 243,
246
+ "CHMP3": 244,
247
+ "CHMP4B": 245,
248
+ "CHMP5": 246,
249
+ "CHMP6": 247,
250
+ "CHMP7": 248,
251
+ "CHORDC1": 249,
252
+ "CHTF18": 250,
253
+ "CHTF8": 251,
254
+ "CHTOP": 252,
255
+ "CIAO1": 253,
256
+ "CIAPIN1": 254,
257
+ "CINP": 255,
258
+ "CKAP5": 256,
259
+ "CLASRP": 257,
260
+ "CLCC1": 258,
261
+ "CLK2": 259,
262
+ "CLNS1A": 260,
263
+ "CLP1": 261,
264
+ "CLSPN": 262,
265
+ "CLTC": 263,
266
+ "CMPK1": 264,
267
+ "CMTR1": 265,
268
+ "CNIH4": 266,
269
+ "CNN2": 267,
270
+ "CNOT1": 268,
271
+ "CNOT2": 269,
272
+ "CNOT3": 270,
273
+ "COA5": 271,
274
+ "COASY": 272,
275
+ "COG1": 273,
276
+ "COG2": 274,
277
+ "COG3": 275,
278
+ "COG4": 276,
279
+ "COG6": 277,
280
+ "COG8": 278,
281
+ "COPA": 279,
282
+ "COPB1": 280,
283
+ "COPB2": 281,
284
+ "COPE": 282,
285
+ "COPG1": 283,
286
+ "COPS2": 284,
287
+ "COPS3": 285,
288
+ "COPS4": 286,
289
+ "COPS5": 287,
290
+ "COPS6": 288,
291
+ "COPS8": 289,
292
+ "COPZ1": 290,
293
+ "COQ2": 291,
294
+ "COQ4": 292,
295
+ "COQ5": 293,
296
+ "COX10": 294,
297
+ "COX11": 295,
298
+ "COX15": 296,
299
+ "COX17": 297,
300
+ "COX5A": 298,
301
+ "COX5B": 299,
302
+ "COX6C": 300,
303
+ "COX7B": 301,
304
+ "COX7C": 302,
305
+ "CPAMD8": 303,
306
+ "CPNE7": 304,
307
+ "CPOX": 305,
308
+ "CPSF1": 306,
309
+ "CPSF2": 307,
310
+ "CPSF3": 308,
311
+ "CPSF4": 309,
312
+ "CPSF6": 310,
313
+ "CRCP": 311,
314
+ "CRKL": 312,
315
+ "CRLS1": 313,
316
+ "CRNKL1": 314,
317
+ "CS": 315,
318
+ "CSE1L": 316,
319
+ "CSH2": 317,
320
+ "CSNK1A1": 318,
321
+ "CSNK2B": 319,
322
+ "CSTF1": 320,
323
+ "CSTF3": 321,
324
+ "CTBP2": 322,
325
+ "CTCF": 323,
326
+ "CTDP1": 324,
327
+ "CTNNBL1": 325,
328
+ "CTPS1": 326,
329
+ "CTR9": 327,
330
+ "CTU2": 328,
331
+ "CUL1": 329,
332
+ "CUL2": 330,
333
+ "CUL3": 331,
334
+ "CUL7": 332,
335
+ "CWC15": 333,
336
+ "CWC22": 334,
337
+ "CWC25": 335,
338
+ "CWF19L2": 336,
339
+ "CXXC1": 337,
340
+ "CYC1": 338,
341
+ "CYCS": 339,
342
+ "CYFIP1": 340,
343
+ "CYP2A13": 341,
344
+ "CYP4F11": 342,
345
+ "CYS1": 343,
346
+ "DAD1": 344,
347
+ "DAP3": 345,
348
+ "DARS": 346,
349
+ "DBF4": 347,
350
+ "DBR1": 348,
351
+ "DCAF6": 349,
352
+ "DCLRE1B": 350,
353
+ "DCTN1": 351,
354
+ "DCTN2": 352,
355
+ "DCTN3": 353,
356
+ "DCTN4": 354,
357
+ "DCTN5": 355,
358
+ "DCTN6": 356,
359
+ "DCUN1D5": 357,
360
+ "DDB1": 358,
361
+ "DDN": 359,
362
+ "DDOST": 360,
363
+ "DDX1": 361,
364
+ "DDX10": 362,
365
+ "DDX11": 363,
366
+ "DDX18": 364,
367
+ "DDX19A": 365,
368
+ "DDX19B": 366,
369
+ "DDX20": 367,
370
+ "DDX21": 368,
371
+ "DDX23": 369,
372
+ "DDX24": 370,
373
+ "DDX27": 371,
374
+ "DDX3X": 372,
375
+ "DDX41": 373,
376
+ "DDX42": 374,
377
+ "DDX46": 375,
378
+ "DDX47": 376,
379
+ "DDX49": 377,
380
+ "DDX5": 378,
381
+ "DDX51": 379,
382
+ "DDX52": 380,
383
+ "DDX54": 381,
384
+ "DDX55": 382,
385
+ "DDX56": 383,
386
+ "DDX59": 384,
387
+ "DDX6": 385,
388
+ "DENR": 386,
389
+ "DERL2": 387,
390
+ "DHDDS": 388,
391
+ "DHFR": 389,
392
+ "DHODH": 390,
393
+ "DHPS": 391,
394
+ "DHX15": 392,
395
+ "DHX16": 393,
396
+ "DHX33": 394,
397
+ "DHX36": 395,
398
+ "DHX37": 396,
399
+ "DHX8": 397,
400
+ "DHX9": 398,
401
+ "DICER1": 399,
402
+ "DIMT1": 400,
403
+ "DIS3": 401,
404
+ "DKC1": 402,
405
+ "DLD": 403,
406
+ "DMAP1": 404,
407
+ "DMRTA2": 405,
408
+ "DNAJA1": 406,
409
+ "DNAJA3": 407,
410
+ "DNAJC11": 408,
411
+ "DNAJC17": 409,
412
+ "DNAJC19": 410,
413
+ "DNAJC8": 411,
414
+ "DNAJC9": 412,
415
+ "DNLZ": 413,
416
+ "DNM1": 414,
417
+ "DNM1L": 415,
418
+ "DNM2": 416,
419
+ "DNMT1": 417,
420
+ "DNTTIP2": 418,
421
+ "DOHH": 419,
422
+ "DOLK": 420,
423
+ "DONSON": 421,
424
+ "DPAGT1": 422,
425
+ "DPH1": 423,
426
+ "DPH2": 424,
427
+ "DPH3": 425,
428
+ "DPH6": 426,
429
+ "DPM2": 427,
430
+ "DPPA2": 428,
431
+ "DPY19L2": 429,
432
+ "DR1": 430,
433
+ "DRAP1": 431,
434
+ "DRG1": 432,
435
+ "DSN1": 433,
436
+ "DTL": 434,
437
+ "DTYMK": 435,
438
+ "DUT": 436,
439
+ "DYNC1H1": 437,
440
+ "DYNC1I2": 438,
441
+ "DYNLL1": 439,
442
+ "DYNLRB1": 440,
443
+ "E2F6": 441,
444
+ "E4F1": 442,
445
+ "EARS2": 443,
446
+ "EBNA1BP2": 444,
447
+ "ECD": 445,
448
+ "ECT2": 446,
449
+ "EDC4": 447,
450
+ "EEF1A1": 448,
451
+ "EEF1B2": 449,
452
+ "EEF1G": 450,
453
+ "EEF2": 451,
454
+ "EFTUD2": 452,
455
+ "EGLN2": 453,
456
+ "EIF1": 454,
457
+ "EIF1AD": 455,
458
+ "EIF1AX": 456,
459
+ "EIF2B1": 457,
460
+ "EIF2B2": 458,
461
+ "EIF2B3": 459,
462
+ "EIF2B4": 460,
463
+ "EIF2B5": 461,
464
+ "EIF2S1": 462,
465
+ "EIF2S2": 463,
466
+ "EIF2S3": 464,
467
+ "EIF3A": 465,
468
+ "EIF3B": 466,
469
+ "EIF3CL": 467,
470
+ "EIF3D": 468,
471
+ "EIF3E": 469,
472
+ "EIF3F": 470,
473
+ "EIF3G": 471,
474
+ "EIF3H": 472,
475
+ "EIF3I": 473,
476
+ "EIF3J": 474,
477
+ "EIF3L": 475,
478
+ "EIF3M": 476,
479
+ "EIF4A1": 477,
480
+ "EIF4A3": 478,
481
+ "EIF4B": 479,
482
+ "EIF4E": 480,
483
+ "EIF4G1": 481,
484
+ "EIF4G2": 482,
485
+ "EIF5": 483,
486
+ "EIF5A": 484,
487
+ "EIF6": 485,
488
+ "ELAC2": 486,
489
+ "ELL": 487,
490
+ "ELOVL1": 488,
491
+ "ELP2": 489,
492
+ "ELP3": 490,
493
+ "ELP5": 491,
494
+ "ELP6": 492,
495
+ "EMC1": 493,
496
+ "EMC3": 494,
497
+ "EMC4": 495,
498
+ "EMC7": 496,
499
+ "ENO1": 497,
500
+ "EP400": 498,
501
+ "EPRS": 499,
502
+ "ERAL1": 500,
503
+ "ERCC2": 501,
504
+ "ERCC3": 502,
505
+ "ERH": 503,
506
+ "ERVW-1": 504,
507
+ "ESF1": 505,
508
+ "ESPL1": 506,
509
+ "ESPN": 507,
510
+ "ETF1": 508,
511
+ "EWSR1": 509,
512
+ "EXOC1": 510,
513
+ "EXOC2": 511,
514
+ "EXOC3": 512,
515
+ "EXOC4": 513,
516
+ "EXOC5": 514,
517
+ "EXOC7": 515,
518
+ "EXOC8": 516,
519
+ "EXOSC1": 517,
520
+ "EXOSC10": 518,
521
+ "EXOSC2": 519,
522
+ "EXOSC3": 520,
523
+ "EXOSC4": 521,
524
+ "EXOSC5": 522,
525
+ "EXOSC6": 523,
526
+ "EXOSC7": 524,
527
+ "EXOSC8": 525,
528
+ "EXOSC9": 526,
529
+ "F8A1": 527,
530
+ "FAF2": 528,
531
+ "FAM133B": 529,
532
+ "FAM136A": 530,
533
+ "FAM207A": 531,
534
+ "FAM229A": 532,
535
+ "FAM32A": 533,
536
+ "FAM50A": 534,
537
+ "FAM72D": 535,
538
+ "FARS2": 536,
539
+ "FARSA": 537,
540
+ "FARSB": 538,
541
+ "FASTKD5": 539,
542
+ "FAU": 540,
543
+ "FBL": 541,
544
+ "FBLIM1": 542,
545
+ "FBXO5": 543,
546
+ "FCF1": 544,
547
+ "FDPS": 545,
548
+ "FDXR": 546,
549
+ "FEN1": 547,
550
+ "FGFR1OP": 548,
551
+ "FIP1L1": 549,
552
+ "FNBP4": 550,
553
+ "FNTA": 551,
554
+ "FNTB": 552,
555
+ "FOLR3": 553,
556
+ "FOXD4": 554,
557
+ "FOXL2": 555,
558
+ "FRG2": 556,
559
+ "FTSJ3": 557,
560
+ "FXN": 558,
561
+ "GAB2": 559,
562
+ "GABPA": 560,
563
+ "GAK": 561,
564
+ "GAPDH": 562,
565
+ "GAR1": 563,
566
+ "GARS": 564,
567
+ "GATA1": 565,
568
+ "GBF1": 566,
569
+ "GCOM1": 567,
570
+ "GEMIN4": 568,
571
+ "GEMIN5": 569,
572
+ "GEMIN6": 570,
573
+ "GEMIN7": 571,
574
+ "GEMIN8": 572,
575
+ "GET1": 573,
576
+ "GET3": 574,
577
+ "GFER": 575,
578
+ "GFM1": 576,
579
+ "GGPS1": 577,
580
+ "GINS1": 578,
581
+ "GINS2": 579,
582
+ "GINS3": 580,
583
+ "GINS4": 581,
584
+ "GIT2": 582,
585
+ "GJA3": 583,
586
+ "GLE1": 584,
587
+ "GLI4": 585,
588
+ "GLMN": 586,
589
+ "GLRX3": 587,
590
+ "GLRX5": 588,
591
+ "GMPPB": 589,
592
+ "GMPS": 590,
593
+ "GNB1L": 591,
594
+ "GNL2": 592,
595
+ "GNL3": 593,
596
+ "GNL3L": 594,
597
+ "GNPNAT1": 595,
598
+ "GOLGA6L1": 596,
599
+ "GOLT1B": 597,
600
+ "GON4L": 598,
601
+ "GOSR2": 599,
602
+ "GPKOW": 600,
603
+ "GPN1": 601,
604
+ "GPN2": 602,
605
+ "GPN3": 603,
606
+ "GPR61": 604,
607
+ "GPS1": 605,
608
+ "GRB2": 606,
609
+ "GRPEL1": 607,
610
+ "GRSF1": 608,
611
+ "GRWD1": 609,
612
+ "GSDMA": 610,
613
+ "GSPT1": 611,
614
+ "GTF2A1": 612,
615
+ "GTF2A2": 613,
616
+ "GTF2B": 614,
617
+ "GTF2E1": 615,
618
+ "GTF2E2": 616,
619
+ "GTF2F1": 617,
620
+ "GTF2F2": 618,
621
+ "GTF2H1": 619,
622
+ "GTF2H2": 620,
623
+ "GTF2H2C": 621,
624
+ "GTF2H3": 622,
625
+ "GTF2H4": 623,
626
+ "GTF3A": 624,
627
+ "GTF3C1": 625,
628
+ "GTF3C2": 626,
629
+ "GTF3C3": 627,
630
+ "GTF3C4": 628,
631
+ "GTF3C5": 629,
632
+ "GTF3C6": 630,
633
+ "GTPBP4": 631,
634
+ "GUCD1": 632,
635
+ "GUK1": 633,
636
+ "H2AFX": 634,
637
+ "H2AFZ": 635,
638
+ "H3F3A": 636,
639
+ "HAMP": 637,
640
+ "HAPLN2": 638,
641
+ "HARS": 639,
642
+ "HARS2": 640,
643
+ "HAUS1": 641,
644
+ "HAUS3": 642,
645
+ "HAUS4": 643,
646
+ "HAUS5": 644,
647
+ "HAUS6": 645,
648
+ "HAUS7": 646,
649
+ "HAUS8": 647,
650
+ "HBS1L": 648,
651
+ "HCFC1": 649,
652
+ "HCRTR1": 650,
653
+ "HDAC3": 651,
654
+ "HDAC7": 652,
655
+ "HEATR1": 653,
656
+ "HECTD1": 654,
657
+ "HGS": 655,
658
+ "HINFP": 656,
659
+ "HIRA": 657,
660
+ "HIST1H2AB": 658,
661
+ "HIST1H2AE": 659,
662
+ "HIST1H2AI": 660,
663
+ "HIST1H2BB": 661,
664
+ "HIST1H2BC": 662,
665
+ "HIST1H2BE": 663,
666
+ "HIST1H2BJ": 664,
667
+ "HIST1H2BL": 665,
668
+ "HIST1H2BM": 666,
669
+ "HIST1H2BN": 667,
670
+ "HIST2H2AA3": 668,
671
+ "HIST2H2AC": 669,
672
+ "HIST2H2BE": 670,
673
+ "HIST2H2BF": 671,
674
+ "HIST2H3A": 672,
675
+ "HIST2H3D": 673,
676
+ "HJURP": 674,
677
+ "HLA-C": 675,
678
+ "HMGA1": 676,
679
+ "HMGB1": 677,
680
+ "HMGCR": 678,
681
+ "HMGCS1": 679,
682
+ "HMGN2": 680,
683
+ "HNRNPC": 681,
684
+ "HNRNPH1": 682,
685
+ "HNRNPK": 683,
686
+ "HNRNPL": 684,
687
+ "HNRNPM": 685,
688
+ "HNRNPR": 686,
689
+ "HNRNPU": 687,
690
+ "HOXC10": 688,
691
+ "HS6ST1": 689,
692
+ "HSCB": 690,
693
+ "HSD17B10": 691,
694
+ "HSD17B12": 692,
695
+ "HSF1": 693,
696
+ "HSP90B1": 694,
697
+ "HSPA14": 695,
698
+ "HSPA5": 696,
699
+ "HSPA8": 697,
700
+ "HSPA9": 698,
701
+ "HSPD1": 699,
702
+ "HSPE1": 700,
703
+ "HTATSF1": 701,
704
+ "HUS1": 702,
705
+ "HUWE1": 703,
706
+ "HYOU1": 704,
707
+ "HYPK": 705,
708
+ "IARS": 706,
709
+ "IARS2": 707,
710
+ "ICE1": 708,
711
+ "IFITM2": 709,
712
+ "IFITM3": 710,
713
+ "IGBP1": 711,
714
+ "IK": 712,
715
+ "ILF2": 713,
716
+ "ILF3": 714,
717
+ "IMP3": 715,
718
+ "IMP4": 716,
719
+ "IMPDH2": 717,
720
+ "INCENP": 718,
721
+ "ING3": 719,
722
+ "INO80": 720,
723
+ "INO80B": 721,
724
+ "INTS1": 722,
725
+ "INTS2": 723,
726
+ "INTS3": 724,
727
+ "INTS4": 725,
728
+ "INTS5": 726,
729
+ "INTS6": 727,
730
+ "INTS7": 728,
731
+ "INTS8": 729,
732
+ "INTS9": 730,
733
+ "IPO11": 731,
734
+ "IPO13": 732,
735
+ "IPO7": 733,
736
+ "IPO9": 734,
737
+ "ISCA2": 735,
738
+ "ISCU": 736,
739
+ "ISG20L2": 737,
740
+ "ISY1": 738,
741
+ "JAZF1": 739,
742
+ "JMJD6": 740,
743
+ "KANSL1": 741,
744
+ "KANSL2": 742,
745
+ "KANSL3": 743,
746
+ "KARS": 744,
747
+ "KAT5": 745,
748
+ "KAT8": 746,
749
+ "KATNB1": 747,
750
+ "KCMF1": 748,
751
+ "KCNA10": 749,
752
+ "KCTD10": 750,
753
+ "KDM2A": 751,
754
+ "KDM8": 752,
755
+ "KIAA1143": 753,
756
+ "KIF11": 754,
757
+ "KIF14": 755,
758
+ "KIF18A": 756,
759
+ "KIF18B": 757,
760
+ "KIF20A": 758,
761
+ "KIF23": 759,
762
+ "KIF4A": 760,
763
+ "KIN": 761,
764
+ "KLC2": 762,
765
+ "KLF7": 763,
766
+ "KLHL11": 764,
767
+ "KPNA6": 765,
768
+ "KPNB1": 766,
769
+ "KRI1": 767,
770
+ "KRR1": 768,
771
+ "KRT10": 769,
772
+ "KRT17": 770,
773
+ "KRT8": 771,
774
+ "KRTAP4-2": 772,
775
+ "KRTAP4-7": 773,
776
+ "KTI12": 774,
777
+ "KXD1": 775,
778
+ "LAMTOR2": 776,
779
+ "LAMTOR3": 777,
780
+ "LAMTOR4": 778,
781
+ "LARS": 779,
782
+ "LARS2": 780,
783
+ "LAS1L": 781,
784
+ "LCE1C": 782,
785
+ "LCE1E": 783,
786
+ "LCN10": 784,
787
+ "LENG8": 785,
788
+ "LETM1": 786,
789
+ "LIMS1": 787,
790
+ "LIN52": 788,
791
+ "LIN54": 789,
792
+ "LONP1": 790,
793
+ "LPA": 791,
794
+ "LRPPRC": 792,
795
+ "LRR1": 793,
796
+ "LRRC37A3": 794,
797
+ "LRRC37B": 795,
798
+ "LSG1": 796,
799
+ "LSM10": 797,
800
+ "LSM11": 798,
801
+ "LSM12": 799,
802
+ "LSM2": 800,
803
+ "LSM3": 801,
804
+ "LSM4": 802,
805
+ "LSM5": 803,
806
+ "LSM6": 804,
807
+ "LSM7": 805,
808
+ "LST1": 806,
809
+ "LTB4R2": 807,
810
+ "LTBP3": 808,
811
+ "LTV1": 809,
812
+ "LUC7L3": 810,
813
+ "LURAP1": 811,
814
+ "LYRM4": 812,
815
+ "MAD2L1": 813,
816
+ "MAD2L2": 814,
817
+ "MAGOH": 815,
818
+ "MAK16": 816,
819
+ "MANF": 817,
820
+ "MARS": 818,
821
+ "MARS2": 819,
822
+ "MASTL": 820,
823
+ "MAT2A": 821,
824
+ "MAU2": 822,
825
+ "MAX": 823,
826
+ "MBTPS1": 824,
827
+ "MBTPS2": 825,
828
+ "MCL1": 826,
829
+ "MCM10": 827,
830
+ "MCM2": 828,
831
+ "MCM3": 829,
832
+ "MCM3AP": 830,
833
+ "MCM4": 831,
834
+ "MCM5": 832,
835
+ "MCM6": 833,
836
+ "MCM7": 834,
837
+ "MCMBP": 835,
838
+ "MCRS1": 836,
839
+ "MDN1": 837,
840
+ "MED1": 838,
841
+ "MED10": 839,
842
+ "MED11": 840,
843
+ "MED12": 841,
844
+ "MED14": 842,
845
+ "MED17": 843,
846
+ "MED18": 844,
847
+ "MED19": 845,
848
+ "MED20": 846,
849
+ "MED21": 847,
850
+ "MED22": 848,
851
+ "MED26": 849,
852
+ "MED27": 850,
853
+ "MED28": 851,
854
+ "MED29": 852,
855
+ "MED30": 853,
856
+ "MED31": 854,
857
+ "MED4": 855,
858
+ "MED6": 856,
859
+ "MED7": 857,
860
+ "MED8": 858,
861
+ "MED9": 859,
862
+ "MEPCE": 860,
863
+ "METAP1": 861,
864
+ "METAP2": 862,
865
+ "METTL1": 863,
866
+ "METTL14": 864,
867
+ "METTL16": 865,
868
+ "METTL17": 866,
869
+ "METTL23": 867,
870
+ "METTL3": 868,
871
+ "MEX3A": 869,
872
+ "MFAP1": 870,
873
+ "MFN2": 871,
874
+ "MICOS10": 872,
875
+ "MIOS": 873,
876
+ "MIPEP": 874,
877
+ "MIS12": 875,
878
+ "MIS18A": 876,
879
+ "MIS18BP1": 877,
880
+ "MKRN1": 878,
881
+ "MLST8": 879,
882
+ "MMGT1": 880,
883
+ "MMS19": 881,
884
+ "MMS22L": 882,
885
+ "MNAT1": 883,
886
+ "MOB4": 884,
887
+ "MOCS3": 885,
888
+ "MOG": 886,
889
+ "MOK": 887,
890
+ "MPHOSPH10": 888,
891
+ "MRGBP": 889,
892
+ "MRPL1": 890,
893
+ "MRPL10": 891,
894
+ "MRPL13": 892,
895
+ "MRPL14": 893,
896
+ "MRPL15": 894,
897
+ "MRPL16": 895,
898
+ "MRPL17": 896,
899
+ "MRPL18": 897,
900
+ "MRPL19": 898,
901
+ "MRPL2": 899,
902
+ "MRPL20": 900,
903
+ "MRPL21": 901,
904
+ "MRPL22": 902,
905
+ "MRPL24": 903,
906
+ "MRPL27": 904,
907
+ "MRPL28": 905,
908
+ "MRPL3": 906,
909
+ "MRPL32": 907,
910
+ "MRPL33": 908,
911
+ "MRPL34": 909,
912
+ "MRPL35": 910,
913
+ "MRPL36": 911,
914
+ "MRPL37": 912,
915
+ "MRPL38": 913,
916
+ "MRPL39": 914,
917
+ "MRPL4": 915,
918
+ "MRPL41": 916,
919
+ "MRPL43": 917,
920
+ "MRPL44": 918,
921
+ "MRPL45": 919,
922
+ "MRPL49": 920,
923
+ "MRPL50": 921,
924
+ "MRPL51": 922,
925
+ "MRPL53": 923,
926
+ "MRPL54": 924,
927
+ "MRPL55": 925,
928
+ "MRPL9": 926,
929
+ "MRPS10": 927,
930
+ "MRPS11": 928,
931
+ "MRPS12": 929,
932
+ "MRPS14": 930,
933
+ "MRPS16": 931,
934
+ "MRPS18A": 932,
935
+ "MRPS18B": 933,
936
+ "MRPS2": 934,
937
+ "MRPS21": 935,
938
+ "MRPS22": 936,
939
+ "MRPS23": 937,
940
+ "MRPS24": 938,
941
+ "MRPS25": 939,
942
+ "MRPS26": 940,
943
+ "MRPS27": 941,
944
+ "MRPS28": 942,
945
+ "MRPS31": 943,
946
+ "MRPS34": 944,
947
+ "MRPS35": 945,
948
+ "MRPS5": 946,
949
+ "MRPS6": 947,
950
+ "MRPS7": 948,
951
+ "MRPS9": 949,
952
+ "MRTO4": 950,
953
+ "MSRB1": 951,
954
+ "MST1": 952,
955
+ "MSTO1": 953,
956
+ "MT2A": 954,
957
+ "MTBP": 955,
958
+ "MTG2": 956,
959
+ "MTOR": 957,
960
+ "MTPAP": 958,
961
+ "MTRNR2L1": 959,
962
+ "MVD": 960,
963
+ "MVK": 961,
964
+ "MYBBP1A": 962,
965
+ "MYBL2": 963,
966
+ "MYC": 964,
967
+ "MYCBP": 965,
968
+ "MYO1H": 966,
969
+ "MZF1": 967,
970
+ "MZT1": 968,
971
+ "N6AMT1": 969,
972
+ "NAA10": 970,
973
+ "NAA15": 971,
974
+ "NAA20": 972,
975
+ "NAA25": 973,
976
+ "NAA35": 974,
977
+ "NAA38": 975,
978
+ "NAA50": 976,
979
+ "NACA": 977,
980
+ "NAE1": 978,
981
+ "NAF1": 979,
982
+ "NAGLU": 980,
983
+ "NAPA": 981,
984
+ "NAPG": 982,
985
+ "NARS": 983,
986
+ "NASP": 984,
987
+ "NAT10": 985,
988
+ "NBAS": 986,
989
+ "NBEAL1": 987,
990
+ "NBPF12": 988,
991
+ "NBPF15": 989,
992
+ "NBPF3": 990,
993
+ "NCAPD2": 991,
994
+ "NCAPD3": 992,
995
+ "NCAPG": 993,
996
+ "NCAPG2": 994,
997
+ "NCAPH": 995,
998
+ "NCAPH2": 996,
999
+ "NCBP1": 997,
1000
+ "NCBP2": 998,
1001
+ "NCKAP1": 999,
1002
+ "NCL": 1000,
1003
+ "NCOA4": 1001,
1004
+ "NDC1": 1002,
1005
+ "NDC80": 1003,
1006
+ "NDOR1": 1004,
1007
+ "NDUFA11": 1005,
1008
+ "NDUFA2": 1006,
1009
+ "NDUFA4": 1007,
1010
+ "NDUFA6": 1008,
1011
+ "NDUFA8": 1009,
1012
+ "NDUFAB1": 1010,
1013
+ "NDUFAF3": 1011,
1014
+ "NDUFAF7": 1012,
1015
+ "NDUFB10": 1013,
1016
+ "NDUFB3": 1014,
1017
+ "NDUFB4": 1015,
1018
+ "NDUFB6": 1016,
1019
+ "NDUFB7": 1017,
1020
+ "NDUFB8": 1018,
1021
+ "NDUFS3": 1019,
1022
+ "NDUFS5": 1020,
1023
+ "NEDD1": 1021,
1024
+ "NEDD8": 1022,
1025
+ "NELFA": 1023,
1026
+ "NELFB": 1024,
1027
+ "NELFCD": 1025,
1028
+ "NELFE": 1026,
1029
+ "NEMF": 1027,
1030
+ "NEPRO": 1028,
1031
+ "NFATC2IP": 1029,
1032
+ "NFKBIE": 1030,
1033
+ "NFRKB": 1031,
1034
+ "NFS1": 1032,
1035
+ "NFYB": 1033,
1036
+ "NFYC": 1034,
1037
+ "NHLRC2": 1035,
1038
+ "NHP2": 1036,
1039
+ "NIFK": 1037,
1040
+ "NIP7": 1038,
1041
+ "NISCH": 1039,
1042
+ "NKAP": 1040,
1043
+ "NLE1": 1041,
1044
+ "NMD3": 1042,
1045
+ "NMT1": 1043,
1046
+ "NOB1": 1044,
1047
+ "NOC2L": 1045,
1048
+ "NOC3L": 1046,
1049
+ "NOC4L": 1047,
1050
+ "NOL10": 1048,
1051
+ "NOL11": 1049,
1052
+ "NOL12": 1050,
1053
+ "NOL6": 1051,
1054
+ "NOL7": 1052,
1055
+ "NOL8": 1053,
1056
+ "NOL9": 1054,
1057
+ "NOLC1": 1055,
1058
+ "NOM1": 1056,
1059
+ "NOMO3": 1057,
1060
+ "NOP10": 1058,
1061
+ "NOP14": 1059,
1062
+ "NOP16": 1060,
1063
+ "NOP2": 1061,
1064
+ "NOP56": 1062,
1065
+ "NOP58": 1063,
1066
+ "NOP9": 1064,
1067
+ "NOS1AP": 1065,
1068
+ "NPAT": 1066,
1069
+ "NPB": 1067,
1070
+ "NPEPPS": 1068,
1071
+ "NPLOC4": 1069,
1072
+ "NPM1": 1070,
1073
+ "NPM3": 1071,
1074
+ "NR2C2AP": 1072,
1075
+ "NRBP1": 1073,
1076
+ "NRDE2": 1074,
1077
+ "NRF1": 1075,
1078
+ "NSA2": 1076,
1079
+ "NSF": 1077,
1080
+ "NSL1": 1078,
1081
+ "NSMCE1": 1079,
1082
+ "NSMCE2": 1080,
1083
+ "NSRP1": 1081,
1084
+ "NSUN4": 1082,
1085
+ "NUBP1": 1083,
1086
+ "NUBP2": 1084,
1087
+ "NUDC": 1085,
1088
+ "NUDCD3": 1086,
1089
+ "NUDT21": 1087,
1090
+ "NUF2": 1088,
1091
+ "NUFIP1": 1089,
1092
+ "NUMA1": 1090,
1093
+ "NUP107": 1091,
1094
+ "NUP133": 1092,
1095
+ "NUP153": 1093,
1096
+ "NUP155": 1094,
1097
+ "NUP160": 1095,
1098
+ "NUP205": 1096,
1099
+ "NUP214": 1097,
1100
+ "NUP35": 1098,
1101
+ "NUP43": 1099,
1102
+ "NUP54": 1100,
1103
+ "NUP62": 1101,
1104
+ "NUP85": 1102,
1105
+ "NUP88": 1103,
1106
+ "NUP93": 1104,
1107
+ "NUP98": 1105,
1108
+ "NUS1": 1106,
1109
+ "NUTF2": 1107,
1110
+ "NVL": 1108,
1111
+ "NXF1": 1109,
1112
+ "OGFOD1": 1110,
1113
+ "OGT": 1111,
1114
+ "OIP5": 1112,
1115
+ "OLFML3": 1113,
1116
+ "OPA1": 1114,
1117
+ "OR1D2": 1115,
1118
+ "OR1E2": 1116,
1119
+ "OR2A1": 1117,
1120
+ "OR2T29": 1118,
1121
+ "OR2T5": 1119,
1122
+ "OR4F4": 1120,
1123
+ "OR4K1": 1121,
1124
+ "OR4N2": 1122,
1125
+ "OR7A10": 1123,
1126
+ "OR7A17": 1124,
1127
+ "ORC1": 1125,
1128
+ "ORC3": 1126,
1129
+ "ORC4": 1127,
1130
+ "ORC5": 1128,
1131
+ "ORC6": 1129,
1132
+ "OSBP": 1130,
1133
+ "OSGEP": 1131,
1134
+ "OSTC": 1132,
1135
+ "OTOP1": 1133,
1136
+ "OTX1": 1134,
1137
+ "OVCA2": 1135,
1138
+ "OXA1L": 1136,
1139
+ "PABPC1": 1137,
1140
+ "PABPN1": 1138,
1141
+ "PAF1": 1139,
1142
+ "PAFAH1B1": 1140,
1143
+ "PAK1IP1": 1141,
1144
+ "PALB2": 1142,
1145
+ "PAM16": 1143,
1146
+ "PARN": 1144,
1147
+ "PARS2": 1145,
1148
+ "PAXBP1": 1146,
1149
+ "PC": 1147,
1150
+ "PCBP1": 1148,
1151
+ "PCBP2": 1149,
1152
+ "PCF11": 1150,
1153
+ "PCID2": 1151,
1154
+ "PCNA": 1152,
1155
+ "PDAP1": 1153,
1156
+ "PDCD11": 1154,
1157
+ "PDCD2": 1155,
1158
+ "PDCD5": 1156,
1159
+ "PDCD6": 1157,
1160
+ "PDCD6IP": 1158,
1161
+ "PDCD7": 1159,
1162
+ "PDPK1": 1160,
1163
+ "PDRG1": 1161,
1164
+ "PEF1": 1162,
1165
+ "PELO": 1163,
1166
+ "PELP1": 1164,
1167
+ "PES1": 1165,
1168
+ "PET117": 1166,
1169
+ "PEX1": 1167,
1170
+ "PFDN1": 1168,
1171
+ "PFDN2": 1169,
1172
+ "PFDN4": 1170,
1173
+ "PFDN5": 1171,
1174
+ "PFDN6": 1172,
1175
+ "PFN1": 1173,
1176
+ "PGAM1": 1174,
1177
+ "PGD": 1175,
1178
+ "PGK1": 1176,
1179
+ "PGPEP1": 1177,
1180
+ "PGS1": 1178,
1181
+ "PHAX": 1179,
1182
+ "PHB": 1180,
1183
+ "PHB2": 1181,
1184
+ "PHF12": 1182,
1185
+ "PHF5A": 1183,
1186
+ "PI4KA": 1184,
1187
+ "PIAS4": 1185,
1188
+ "PIGH": 1186,
1189
+ "PIK3C3": 1187,
1190
+ "PIK3R4": 1188,
1191
+ "PKM": 1189,
1192
+ "PKMYT1": 1190,
1193
+ "PLA2G10": 1191,
1194
+ "PLEKHN1": 1192,
1195
+ "PLK1": 1193,
1196
+ "PLK4": 1194,
1197
+ "PLRG1": 1195,
1198
+ "PMF1": 1196,
1199
+ "PMPCA": 1197,
1200
+ "PMPCB": 1198,
1201
+ "PNISR": 1199,
1202
+ "PNKP": 1200,
1203
+ "PNN": 1201,
1204
+ "PNO1": 1202,
1205
+ "PNPT1": 1203,
1206
+ "POGZ": 1204,
1207
+ "POLA1": 1205,
1208
+ "POLA2": 1206,
1209
+ "POLD1": 1207,
1210
+ "POLD2": 1208,
1211
+ "POLD3": 1209,
1212
+ "POLE": 1210,
1213
+ "POLE2": 1211,
1214
+ "POLG2": 1212,
1215
+ "POLR1A": 1213,
1216
+ "POLR1B": 1214,
1217
+ "POLR1C": 1215,
1218
+ "POLR1E": 1216,
1219
+ "POLR2A": 1217,
1220
+ "POLR2B": 1218,
1221
+ "POLR2C": 1219,
1222
+ "POLR2D": 1220,
1223
+ "POLR2E": 1221,
1224
+ "POLR2F": 1222,
1225
+ "POLR2G": 1223,
1226
+ "POLR2H": 1224,
1227
+ "POLR2I": 1225,
1228
+ "POLR2K": 1226,
1229
+ "POLR2L": 1227,
1230
+ "POLR3A": 1228,
1231
+ "POLR3B": 1229,
1232
+ "POLR3C": 1230,
1233
+ "POLR3D": 1231,
1234
+ "POLR3E": 1232,
1235
+ "POLR3F": 1233,
1236
+ "POLR3H": 1234,
1237
+ "POLR3K": 1235,
1238
+ "POLRMT": 1236,
1239
+ "POP1": 1237,
1240
+ "POP4": 1238,
1241
+ "POP5": 1239,
1242
+ "POP7": 1240,
1243
+ "POT1": 1241,
1244
+ "POTEI": 1242,
1245
+ "POU5F1B": 1243,
1246
+ "PPA1": 1244,
1247
+ "PPA2": 1245,
1248
+ "PPAN": 1246,
1249
+ "PPARGC1B": 1247,
1250
+ "PPIA": 1248,
1251
+ "PPIE": 1249,
1252
+ "PPIH": 1250,
1253
+ "PPIL1": 1251,
1254
+ "PPIL2": 1252,
1255
+ "PPIL4": 1253,
1256
+ "PPME1": 1254,
1257
+ "PPP1CA": 1255,
1258
+ "PPP1CB": 1256,
1259
+ "PPP1R10": 1257,
1260
+ "PPP1R11": 1258,
1261
+ "PPP1R12A": 1259,
1262
+ "PPP1R15B": 1260,
1263
+ "PPP1R2": 1261,
1264
+ "PPP1R7": 1262,
1265
+ "PPP1R8": 1263,
1266
+ "PPP2CA": 1264,
1267
+ "PPP2R1A": 1265,
1268
+ "PPP2R3C": 1266,
1269
+ "PPP4C": 1267,
1270
+ "PPP4R2": 1268,
1271
+ "PPP6C": 1269,
1272
+ "PPRC1": 1270,
1273
+ "PPWD1": 1271,
1274
+ "PPY": 1272,
1275
+ "PRC1": 1273,
1276
+ "PRDM10": 1274,
1277
+ "PREB": 1275,
1278
+ "PRELID1": 1276,
1279
+ "PRELID3B": 1277,
1280
+ "PRIM1": 1278,
1281
+ "PRIM2": 1279,
1282
+ "PRKRA": 1280,
1283
+ "PRKRIP1": 1281,
1284
+ "PRMT1": 1282,
1285
+ "PRMT5": 1283,
1286
+ "PRODH": 1284,
1287
+ "PRORP": 1285,
1288
+ "PRPF18": 1286,
1289
+ "PRPF19": 1287,
1290
+ "PRPF3": 1288,
1291
+ "PRPF31": 1289,
1292
+ "PRPF38A": 1290,
1293
+ "PRPF38B": 1291,
1294
+ "PRPF4": 1292,
1295
+ "PRPF40A": 1293,
1296
+ "PRPF4B": 1294,
1297
+ "PRPF6": 1295,
1298
+ "PRPF8": 1296,
1299
+ "PRRC2A": 1297,
1300
+ "PSAT1": 1298,
1301
+ "PSMA1": 1299,
1302
+ "PSMA2": 1300,
1303
+ "PSMA3": 1301,
1304
+ "PSMA4": 1302,
1305
+ "PSMA5": 1303,
1306
+ "PSMA6": 1304,
1307
+ "PSMA7": 1305,
1308
+ "PSMB1": 1306,
1309
+ "PSMB2": 1307,
1310
+ "PSMB3": 1308,
1311
+ "PSMB4": 1309,
1312
+ "PSMB5": 1310,
1313
+ "PSMB6": 1311,
1314
+ "PSMB7": 1312,
1315
+ "PSMC1": 1313,
1316
+ "PSMC2": 1314,
1317
+ "PSMC3": 1315,
1318
+ "PSMC4": 1316,
1319
+ "PSMC5": 1317,
1320
+ "PSMC6": 1318,
1321
+ "PSMD1": 1319,
1322
+ "PSMD11": 1320,
1323
+ "PSMD12": 1321,
1324
+ "PSMD13": 1322,
1325
+ "PSMD14": 1323,
1326
+ "PSMD2": 1324,
1327
+ "PSMD3": 1325,
1328
+ "PSMD4": 1326,
1329
+ "PSMD6": 1327,
1330
+ "PSMD7": 1328,
1331
+ "PSMD8": 1329,
1332
+ "PSMD9": 1330,
1333
+ "PSME1": 1331,
1334
+ "PSME2": 1332,
1335
+ "PSMG1": 1333,
1336
+ "PSMG2": 1334,
1337
+ "PSMG3": 1335,
1338
+ "PSMG4": 1336,
1339
+ "PSTK": 1337,
1340
+ "PTBP1": 1338,
1341
+ "PTCD1": 1339,
1342
+ "PTCD3": 1340,
1343
+ "PTK2": 1341,
1344
+ "PTMA": 1342,
1345
+ "PTPMT1": 1343,
1346
+ "PTPN23": 1344,
1347
+ "PUF60": 1345,
1348
+ "PWP1": 1346,
1349
+ "PWP2": 1347,
1350
+ "PXN": 1348,
1351
+ "PYROXD1": 1349,
1352
+ "QARS": 1350,
1353
+ "QRSL1": 1351,
1354
+ "RAB18": 1352,
1355
+ "RAB4A": 1353,
1356
+ "RAB6A": 1354,
1357
+ "RABGGTA": 1355,
1358
+ "RABGGTB": 1356,
1359
+ "RAC1": 1357,
1360
+ "RAC3": 1358,
1361
+ "RACGAP1": 1359,
1362
+ "RAD17": 1360,
1363
+ "RAD21": 1361,
1364
+ "RAD51": 1362,
1365
+ "RAD51C": 1363,
1366
+ "RAD51D": 1364,
1367
+ "RAD9A": 1365,
1368
+ "RAE1": 1366,
1369
+ "RAN": 1367,
1370
+ "RANBP2": 1368,
1371
+ "RANGAP1": 1369,
1372
+ "RARS": 1370,
1373
+ "RARS2": 1371,
1374
+ "RBBP4": 1372,
1375
+ "RBBP5": 1373,
1376
+ "RBBP6": 1374,
1377
+ "RBBP8": 1375,
1378
+ "RBM10": 1376,
1379
+ "RBM14": 1377,
1380
+ "RBM17": 1378,
1381
+ "RBM19": 1379,
1382
+ "RBM22": 1380,
1383
+ "RBM25": 1381,
1384
+ "RBM28": 1382,
1385
+ "RBM39": 1383,
1386
+ "RBM4": 1384,
1387
+ "RBM42": 1385,
1388
+ "RBM48": 1386,
1389
+ "RBM8A": 1387,
1390
+ "RBMX": 1388,
1391
+ "RBMX2": 1389,
1392
+ "RBMXL1": 1390,
1393
+ "RBX1": 1391,
1394
+ "RCC1": 1392,
1395
+ "RCL1": 1393,
1396
+ "RCOR1": 1394,
1397
+ "REV3L": 1395,
1398
+ "REXO2": 1396,
1399
+ "RFC1": 1397,
1400
+ "RFC2": 1398,
1401
+ "RFC3": 1399,
1402
+ "RFC4": 1400,
1403
+ "RFC5": 1401,
1404
+ "RFFL": 1402,
1405
+ "RFT1": 1403,
1406
+ "RGP1": 1404,
1407
+ "RGPD6": 1405,
1408
+ "RHOQ": 1406,
1409
+ "RHPN1": 1407,
1410
+ "RINT1": 1408,
1411
+ "RIOK1": 1409,
1412
+ "RIOK2": 1410,
1413
+ "RMI1": 1411,
1414
+ "RNASEH2C": 1412,
1415
+ "RNF103": 1413,
1416
+ "RNF113A": 1414,
1417
+ "RNF123": 1415,
1418
+ "RNF14": 1416,
1419
+ "RNF168": 1417,
1420
+ "RNF20": 1418,
1421
+ "RNF4": 1419,
1422
+ "RNF40": 1420,
1423
+ "RNF8": 1421,
1424
+ "RNGTT": 1422,
1425
+ "RNMT": 1423,
1426
+ "RNPC3": 1424,
1427
+ "RNPS1": 1425,
1428
+ "ROMO1": 1426,
1429
+ "RPA1": 1427,
1430
+ "RPA2": 1428,
1431
+ "RPA3": 1429,
1432
+ "RPAIN": 1430,
1433
+ "RPAP1": 1431,
1434
+ "RPAP2": 1432,
1435
+ "RPAP3": 1433,
1436
+ "RPE": 1434,
1437
+ "RPF1": 1435,
1438
+ "RPF2": 1436,
1439
+ "RPL10": 1437,
1440
+ "RPL10A": 1438,
1441
+ "RPL11": 1439,
1442
+ "RPL12": 1440,
1443
+ "RPL13": 1441,
1444
+ "RPL13A": 1442,
1445
+ "RPL14": 1443,
1446
+ "RPL15": 1444,
1447
+ "RPL17": 1445,
1448
+ "RPL18": 1446,
1449
+ "RPL18A": 1447,
1450
+ "RPL19": 1448,
1451
+ "RPL21": 1449,
1452
+ "RPL23": 1450,
1453
+ "RPL23A": 1451,
1454
+ "RPL24": 1452,
1455
+ "RPL26": 1453,
1456
+ "RPL26L1": 1454,
1457
+ "RPL27": 1455,
1458
+ "RPL27A": 1456,
1459
+ "RPL28": 1457,
1460
+ "RPL29": 1458,
1461
+ "RPL3": 1459,
1462
+ "RPL30": 1460,
1463
+ "RPL31": 1461,
1464
+ "RPL32": 1462,
1465
+ "RPL34": 1463,
1466
+ "RPL35": 1464,
1467
+ "RPL35A": 1465,
1468
+ "RPL36": 1466,
1469
+ "RPL36A": 1467,
1470
+ "RPL36AL": 1468,
1471
+ "RPL37": 1469,
1472
+ "RPL37A": 1470,
1473
+ "RPL38": 1471,
1474
+ "RPL39": 1472,
1475
+ "RPL4": 1473,
1476
+ "RPL41": 1474,
1477
+ "RPL5": 1475,
1478
+ "RPL6": 1476,
1479
+ "RPL7": 1477,
1480
+ "RPL7A": 1478,
1481
+ "RPL7L1": 1479,
1482
+ "RPL8": 1480,
1483
+ "RPL9": 1481,
1484
+ "RPLP0": 1482,
1485
+ "RPLP1": 1483,
1486
+ "RPLP2": 1484,
1487
+ "RPN1": 1485,
1488
+ "RPN2": 1486,
1489
+ "RPP14": 1487,
1490
+ "RPP21": 1488,
1491
+ "RPP30": 1489,
1492
+ "RPP38": 1490,
1493
+ "RPP40": 1491,
1494
+ "RPS10": 1492,
1495
+ "RPS10-NUDT3": 1493,
1496
+ "RPS11": 1494,
1497
+ "RPS12": 1495,
1498
+ "RPS13": 1496,
1499
+ "RPS14": 1497,
1500
+ "RPS15": 1498,
1501
+ "RPS15A": 1499,
1502
+ "RPS16": 1500,
1503
+ "RPS17": 1501,
1504
+ "RPS18": 1502,
1505
+ "RPS19": 1503,
1506
+ "RPS19BP1": 1504,
1507
+ "RPS2": 1505,
1508
+ "RPS20": 1506,
1509
+ "RPS21": 1507,
1510
+ "RPS23": 1508,
1511
+ "RPS24": 1509,
1512
+ "RPS25": 1510,
1513
+ "RPS26": 1511,
1514
+ "RPS27": 1512,
1515
+ "RPS27A": 1513,
1516
+ "RPS28": 1514,
1517
+ "RPS29": 1515,
1518
+ "RPS3": 1516,
1519
+ "RPS3A": 1517,
1520
+ "RPS4X": 1518,
1521
+ "RPS5": 1519,
1522
+ "RPS6": 1520,
1523
+ "RPS7": 1521,
1524
+ "RPS8": 1522,
1525
+ "RPS9": 1523,
1526
+ "RPSA": 1524,
1527
+ "RPTOR": 1525,
1528
+ "RPUSD3": 1526,
1529
+ "RPUSD4": 1527,
1530
+ "RRM1": 1528,
1531
+ "RRM2": 1529,
1532
+ "RRN3": 1530,
1533
+ "RRP1": 1531,
1534
+ "RRP12": 1532,
1535
+ "RRP15": 1533,
1536
+ "RRP7A": 1534,
1537
+ "RRP9": 1535,
1538
+ "RRS1": 1536,
1539
+ "RSL1D1": 1537,
1540
+ "RSL24D1": 1538,
1541
+ "RSRC2": 1539,
1542
+ "RTCB": 1540,
1543
+ "RTEL1": 1541,
1544
+ "RTF1": 1542,
1545
+ "RTTN": 1543,
1546
+ "RUVBL1": 1544,
1547
+ "RUVBL2": 1545,
1548
+ "SACM1L": 1546,
1549
+ "SAE1": 1547,
1550
+ "SAMM50": 1548,
1551
+ "SAP130": 1549,
1552
+ "SAP18": 1550,
1553
+ "SAP30BP": 1551,
1554
+ "SARNP": 1552,
1555
+ "SARS": 1553,
1556
+ "SARS2": 1554,
1557
+ "SART1": 1555,
1558
+ "SART3": 1556,
1559
+ "SASS6": 1557,
1560
+ "SBDS": 1558,
1561
+ "SBNO1": 1559,
1562
+ "SCAF1": 1560,
1563
+ "SCAP": 1561,
1564
+ "SCD": 1562,
1565
+ "SCFD1": 1563,
1566
+ "SCNM1": 1564,
1567
+ "SDAD1": 1565,
1568
+ "SDC1": 1566,
1569
+ "SDE2": 1567,
1570
+ "SDHA": 1568,
1571
+ "SDHAF2": 1569,
1572
+ "SDHC": 1570,
1573
+ "SDHD": 1571,
1574
+ "SEC13": 1572,
1575
+ "SEC16A": 1573,
1576
+ "SEC61A1": 1574,
1577
+ "SEC61B": 1575,
1578
+ "SEC61G": 1576,
1579
+ "SEC62": 1577,
1580
+ "SEC63": 1578,
1581
+ "SEH1L": 1579,
1582
+ "SEM1": 1580,
1583
+ "SENP6": 1581,
1584
+ "SEPHS2": 1582,
1585
+ "SEPSECS": 1583,
1586
+ "SERBP1": 1584,
1587
+ "SET": 1585,
1588
+ "SETD1A": 1586,
1589
+ "SETD2": 1587,
1590
+ "SETDB1": 1588,
1591
+ "SF1": 1589,
1592
+ "SF3A1": 1590,
1593
+ "SF3A2": 1591,
1594
+ "SF3A3": 1592,
1595
+ "SF3B1": 1593,
1596
+ "SF3B2": 1594,
1597
+ "SF3B3": 1595,
1598
+ "SF3B4": 1596,
1599
+ "SF3B5": 1597,
1600
+ "SFPQ": 1598,
1601
+ "SFSWAP": 1599,
1602
+ "SGPP1": 1600,
1603
+ "SHQ1": 1601,
1604
+ "SIGLEC14": 1602,
1605
+ "SIN3A": 1603,
1606
+ "SKA1": 1604,
1607
+ "SKA3": 1605,
1608
+ "SKP1": 1606,
1609
+ "SKP2": 1607,
1610
+ "SLBP": 1608,
1611
+ "SLC16A5": 1609,
1612
+ "SLC1A5": 1610,
1613
+ "SLC25A10": 1611,
1614
+ "SLC25A26": 1612,
1615
+ "SLC25A3": 1613,
1616
+ "SLC35B1": 1614,
1617
+ "SLC35G6": 1615,
1618
+ "SLC39A10": 1616,
1619
+ "SLC39A7": 1617,
1620
+ "SLC39A9": 1618,
1621
+ "SLC4A5": 1619,
1622
+ "SLC7A5": 1620,
1623
+ "SLC7A6OS": 1621,
1624
+ "SLC9B1": 1622,
1625
+ "SLU7": 1623,
1626
+ "SMAGP": 1624,
1627
+ "SMARCB1": 1625,
1628
+ "SMARCE1": 1626,
1629
+ "SMC1A": 1627,
1630
+ "SMC2": 1628,
1631
+ "SMC3": 1629,
1632
+ "SMC4": 1630,
1633
+ "SMC5": 1631,
1634
+ "SMC6": 1632,
1635
+ "SMG1": 1633,
1636
+ "SMG5": 1634,
1637
+ "SMG6": 1635,
1638
+ "SMN2": 1636,
1639
+ "SMNDC1": 1637,
1640
+ "SMU1": 1638,
1641
+ "SMUG1": 1639,
1642
+ "SNAPC1": 1640,
1643
+ "SNAPC2": 1641,
1644
+ "SNAPC3": 1642,
1645
+ "SNAPC4": 1643,
1646
+ "SNAPC5": 1644,
1647
+ "SNF8": 1645,
1648
+ "SNIP1": 1646,
1649
+ "SNRNP200": 1647,
1650
+ "SNRNP25": 1648,
1651
+ "SNRNP27": 1649,
1652
+ "SNRNP35": 1650,
1653
+ "SNRNP40": 1651,
1654
+ "SNRNP48": 1652,
1655
+ "SNRNP70": 1653,
1656
+ "SNRPA1": 1654,
1657
+ "SNRPB": 1655,
1658
+ "SNRPC": 1656,
1659
+ "SNRPD1": 1657,
1660
+ "SNRPD2": 1658,
1661
+ "SNRPD3": 1659,
1662
+ "SNRPE": 1660,
1663
+ "SNRPF": 1661,
1664
+ "SNRPG": 1662,
1665
+ "SNUPN": 1663,
1666
+ "SNW1": 1664,
1667
+ "SNX15": 1665,
1668
+ "SOD1": 1666,
1669
+ "SOD2": 1667,
1670
+ "SON": 1668,
1671
+ "SP2": 1669,
1672
+ "SPATA5": 1670,
1673
+ "SPATA5L1": 1671,
1674
+ "SPC24": 1672,
1675
+ "SPC25": 1673,
1676
+ "SPCS2": 1674,
1677
+ "SPCS3": 1675,
1678
+ "SPDL1": 1676,
1679
+ "SPDYE2": 1677,
1680
+ "SPRTN": 1678,
1681
+ "SPTLC1": 1679,
1682
+ "SPTSSA": 1680,
1683
+ "SRBD1": 1681,
1684
+ "SRCAP": 1682,
1685
+ "SRF": 1683,
1686
+ "SRFBP1": 1684,
1687
+ "SRP14": 1685,
1688
+ "SRP19": 1686,
1689
+ "SRP54": 1687,
1690
+ "SRP68": 1688,
1691
+ "SRP72": 1689,
1692
+ "SRP9": 1690,
1693
+ "SRPRB": 1691,
1694
+ "SRRM1": 1692,
1695
+ "SRRM2": 1693,
1696
+ "SRRT": 1694,
1697
+ "SRSF1": 1695,
1698
+ "SRSF10": 1696,
1699
+ "SRSF11": 1697,
1700
+ "SRSF2": 1698,
1701
+ "SRSF3": 1699,
1702
+ "SRSF6": 1700,
1703
+ "SRSF7": 1701,
1704
+ "SS18L2": 1702,
1705
+ "SSBP1": 1703,
1706
+ "SSBP3": 1704,
1707
+ "SSRP1": 1705,
1708
+ "SSU72": 1706,
1709
+ "SSX4": 1707,
1710
+ "STARD7": 1708,
1711
+ "STAT5A": 1709,
1712
+ "STIL": 1710,
1713
+ "STRAP": 1711,
1714
+ "STRIP1": 1712,
1715
+ "STX18": 1713,
1716
+ "STX5": 1714,
1717
+ "SUGP1": 1715,
1718
+ "SUGT1": 1716,
1719
+ "SUMO2": 1717,
1720
+ "SUPT16H": 1718,
1721
+ "SUPT4H1": 1719,
1722
+ "SUPT5H": 1720,
1723
+ "SUPT6H": 1721,
1724
+ "SUPV3L1": 1722,
1725
+ "SURF6": 1723,
1726
+ "SYF2": 1724,
1727
+ "SYMPK": 1725,
1728
+ "SYS1": 1726,
1729
+ "TACC3": 1727,
1730
+ "TADA2A": 1728,
1731
+ "TADA3": 1729,
1732
+ "TAF1": 1730,
1733
+ "TAF10": 1731,
1734
+ "TAF12": 1732,
1735
+ "TAF1B": 1733,
1736
+ "TAF1C": 1734,
1737
+ "TAF1D": 1735,
1738
+ "TAF2": 1736,
1739
+ "TAF5": 1737,
1740
+ "TAF6": 1738,
1741
+ "TAF7": 1739,
1742
+ "TAF8": 1740,
1743
+ "TAMM41": 1741,
1744
+ "TANGO6": 1742,
1745
+ "TARDBP": 1743,
1746
+ "TARS": 1744,
1747
+ "TARS2": 1745,
1748
+ "TBC1D28": 1746,
1749
+ "TBC1D3": 1747,
1750
+ "TBCA": 1748,
1751
+ "TBCB": 1749,
1752
+ "TBCC": 1750,
1753
+ "TBCD": 1751,
1754
+ "TBCE": 1752,
1755
+ "TBL3": 1753,
1756
+ "TBP": 1754,
1757
+ "TCERG1": 1755,
1758
+ "TCOF1": 1756,
1759
+ "TCP1": 1757,
1760
+ "TDGF1": 1758,
1761
+ "TEAD3": 1759,
1762
+ "TEFM": 1760,
1763
+ "TELO2": 1761,
1764
+ "TEN1": 1762,
1765
+ "TERF1": 1763,
1766
+ "TERF2": 1764,
1767
+ "TEX10": 1765,
1768
+ "TFAM": 1766,
1769
+ "TFB2M": 1767,
1770
+ "TFDP1": 1768,
1771
+ "TFIP11": 1769,
1772
+ "TFRC": 1770,
1773
+ "TGS1": 1771,
1774
+ "THAP1": 1772,
1775
+ "THAP11": 1773,
1776
+ "THG1L": 1774,
1777
+ "THOC1": 1775,
1778
+ "THOC2": 1776,
1779
+ "THOC3": 1777,
1780
+ "THOC5": 1778,
1781
+ "THOC6": 1779,
1782
+ "THOC7": 1780,
1783
+ "TICRR": 1781,
1784
+ "TIGD1": 1782,
1785
+ "TIMELESS": 1783,
1786
+ "TIMM10": 1784,
1787
+ "TIMM13": 1785,
1788
+ "TIMM22": 1786,
1789
+ "TIMM23B": 1787,
1790
+ "TIMM44": 1788,
1791
+ "TIMM8A": 1789,
1792
+ "TIMM9": 1790,
1793
+ "TINF2": 1791,
1794
+ "TIPIN": 1792,
1795
+ "TKT": 1793,
1796
+ "TLCD1": 1794,
1797
+ "TLN1": 1795,
1798
+ "TM7SF2": 1796,
1799
+ "TMA16": 1797,
1800
+ "TMED2": 1798,
1801
+ "TMEM127": 1799,
1802
+ "TMEM199": 1800,
1803
+ "TMEM240": 1801,
1804
+ "TMEM258": 1802,
1805
+ "TMSB10": 1803,
1806
+ "TMX2": 1804,
1807
+ "TNNT2": 1805,
1808
+ "TNPO3": 1806,
1809
+ "TOE1": 1807,
1810
+ "TOMM20": 1808,
1811
+ "TOMM22": 1809,
1812
+ "TOMM40": 1810,
1813
+ "TONSL": 1811,
1814
+ "TOP1": 1812,
1815
+ "TOP2A": 1813,
1816
+ "TOP3A": 1814,
1817
+ "TOPBP1": 1815,
1818
+ "TOR2A": 1816,
1819
+ "TP53RK": 1817,
1820
+ "TPI1": 1818,
1821
+ "TPR": 1819,
1822
+ "TPRKB": 1820,
1823
+ "TPT1": 1821,
1824
+ "TPX2": 1822,
1825
+ "TRA2B": 1823,
1826
+ "TRAIP": 1824,
1827
+ "TRAPPC1": 1825,
1828
+ "TRAPPC11": 1826,
1829
+ "TRAPPC3": 1827,
1830
+ "TRAPPC4": 1828,
1831
+ "TRAPPC5": 1829,
1832
+ "TRAPPC8": 1830,
1833
+ "TREML2": 1831,
1834
+ "TREX2": 1832,
1835
+ "TRIAP1": 1833,
1836
+ "TRIM49C": 1834,
1837
+ "TRMT10C": 1835,
1838
+ "TRMT112": 1836,
1839
+ "TRMT5": 1837,
1840
+ "TRMT6": 1838,
1841
+ "TRNP1": 1839,
1842
+ "TRNT1": 1840,
1843
+ "TRPM7": 1841,
1844
+ "TRRAP": 1842,
1845
+ "TSEN2": 1843,
1846
+ "TSEN34": 1844,
1847
+ "TSEN54": 1845,
1848
+ "TSFM": 1846,
1849
+ "TSG101": 1847,
1850
+ "TSPYL5": 1848,
1851
+ "TSR1": 1849,
1852
+ "TSR2": 1850,
1853
+ "TSSK3": 1851,
1854
+ "TTC1": 1852,
1855
+ "TTC27": 1853,
1856
+ "TTC4": 1854,
1857
+ "TTF2": 1855,
1858
+ "TTI1": 1856,
1859
+ "TTI2": 1857,
1860
+ "TTK": 1858,
1861
+ "TUBA1B": 1859,
1862
+ "TUBA1C": 1860,
1863
+ "TUBA3D": 1861,
1864
+ "TUBB": 1862,
1865
+ "TUBD1": 1863,
1866
+ "TUBE1": 1864,
1867
+ "TUBG1": 1865,
1868
+ "TUBGCP2": 1866,
1869
+ "TUBGCP3": 1867,
1870
+ "TUBGCP4": 1868,
1871
+ "TUBGCP5": 1869,
1872
+ "TUBGCP6": 1870,
1873
+ "TULP1": 1871,
1874
+ "TUT1": 1872,
1875
+ "TVP23C": 1873,
1876
+ "TWF1": 1874,
1877
+ "TWISTNB": 1875,
1878
+ "TXN": 1876,
1879
+ "TXNL4A": 1877,
1880
+ "TXNL4B": 1878,
1881
+ "U2AF1": 1879,
1882
+ "U2AF2": 1880,
1883
+ "U2SURP": 1881,
1884
+ "UBA1": 1882,
1885
+ "UBA2": 1883,
1886
+ "UBA3": 1884,
1887
+ "UBA5": 1885,
1888
+ "UBA52": 1886,
1889
+ "UBAP1": 1887,
1890
+ "UBC": 1888,
1891
+ "UBE2D3": 1889,
1892
+ "UBE2H": 1890,
1893
+ "UBE2I": 1891,
1894
+ "UBE2L3": 1892,
1895
+ "UBE2M": 1893,
1896
+ "UBE2N": 1894,
1897
+ "UBE2Z": 1895,
1898
+ "UBL5": 1896,
1899
+ "UBQLN4": 1897,
1900
+ "UBR4": 1898,
1901
+ "UBR5": 1899,
1902
+ "UBTF": 1900,
1903
+ "UFL1": 1901,
1904
+ "UFM1": 1902,
1905
+ "UNC45A": 1903,
1906
+ "UNC50": 1904,
1907
+ "UPF1": 1905,
1908
+ "UPF2": 1906,
1909
+ "UPF3A": 1907,
1910
+ "UQCC2": 1908,
1911
+ "UQCRB": 1909,
1912
+ "UQCRC1": 1910,
1913
+ "UQCRC2": 1911,
1914
+ "UQCRFS1": 1912,
1915
+ "UQCRH": 1913,
1916
+ "UQCRQ": 1914,
1917
+ "URB1": 1915,
1918
+ "URB2": 1916,
1919
+ "URI1": 1917,
1920
+ "URM1": 1918,
1921
+ "UROD": 1919,
1922
+ "USF2": 1920,
1923
+ "USP10": 1921,
1924
+ "USP19": 1922,
1925
+ "USP36": 1923,
1926
+ "USP37": 1924,
1927
+ "USP39": 1925,
1928
+ "USP5": 1926,
1929
+ "USP7": 1927,
1930
+ "USP8": 1928,
1931
+ "USP9X": 1929,
1932
+ "USPL1": 1930,
1933
+ "UTP15": 1931,
1934
+ "UTP18": 1932,
1935
+ "UTP20": 1933,
1936
+ "UTP23": 1934,
1937
+ "UTP3": 1935,
1938
+ "UTP6": 1936,
1939
+ "UXS1": 1937,
1940
+ "UXT": 1938,
1941
+ "VARS": 1939,
1942
+ "VARS2": 1940,
1943
+ "VBP1": 1941,
1944
+ "VCP": 1942,
1945
+ "VEZT": 1943,
1946
+ "VHL": 1944,
1947
+ "VMP1": 1945,
1948
+ "VPS13D": 1946,
1949
+ "VPS18": 1947,
1950
+ "VPS25": 1948,
1951
+ "VPS28": 1949,
1952
+ "VPS29": 1950,
1953
+ "VPS33A": 1951,
1954
+ "VPS35": 1952,
1955
+ "VPS37A": 1953,
1956
+ "VPS37C": 1954,
1957
+ "VPS41": 1955,
1958
+ "VPS51": 1956,
1959
+ "VPS54": 1957,
1960
+ "VPS72": 1958,
1961
+ "WAC": 1959,
1962
+ "WARS": 1960,
1963
+ "WBP1": 1961,
1964
+ "WBP11": 1962,
1965
+ "WBP1L": 1963,
1966
+ "WDHD1": 1964,
1967
+ "WDR1": 1965,
1968
+ "WDR12": 1966,
1969
+ "WDR18": 1967,
1970
+ "WDR24": 1968,
1971
+ "WDR25": 1969,
1972
+ "WDR26": 1970,
1973
+ "WDR3": 1971,
1974
+ "WDR33": 1972,
1975
+ "WDR36": 1973,
1976
+ "WDR4": 1974,
1977
+ "WDR43": 1975,
1978
+ "WDR46": 1976,
1979
+ "WDR5": 1977,
1980
+ "WDR54": 1978,
1981
+ "WDR55": 1979,
1982
+ "WDR61": 1980,
1983
+ "WDR7": 1981,
1984
+ "WDR70": 1982,
1985
+ "WDR74": 1983,
1986
+ "WDR75": 1984,
1987
+ "WDR77": 1985,
1988
+ "WDR82": 1986,
1989
+ "WDR83OS": 1987,
1990
+ "WDR92": 1988,
1991
+ "WDTC1": 1989,
1992
+ "WEE1": 1990,
1993
+ "WNK1": 1991,
1994
+ "WTAP": 1992,
1995
+ "XAB2": 1993,
1996
+ "XPO1": 1994,
1997
+ "XPO5": 1995,
1998
+ "XRCC1": 1996,
1999
+ "XRCC2": 1997,
2000
+ "XRCC3": 1998,
2001
+ "XRCC5": 1999,
2002
+ "XRCC6": 2000,
2003
+ "XRN1": 2001,
2004
+ "XRN2": 2002,
2005
+ "YARS": 2003,
2006
+ "YARS2": 2004,
2007
+ "YBX1": 2005,
2008
+ "YEATS2": 2006,
2009
+ "YEATS4": 2007,
2010
+ "YJEFN3": 2008,
2011
+ "YKT6": 2009,
2012
+ "YPEL1": 2010,
2013
+ "YPEL5": 2011,
2014
+ "YRDC": 2012,
2015
+ "YTHDC1": 2013,
2016
+ "YY1": 2014,
2017
+ "ZBTB11": 2015,
2018
+ "ZBTB17": 2016,
2019
+ "ZC3H18": 2017,
2020
+ "ZC3H8": 2018,
2021
+ "ZCCHC9": 2019,
2022
+ "ZCRB1": 2020,
2023
+ "ZFC3H1": 2021,
2024
+ "ZFP69B": 2022,
2025
+ "ZMAT2": 2023,
2026
+ "ZMAT5": 2024,
2027
+ "ZNF100": 2025,
2028
+ "ZNF131": 2026,
2029
+ "ZNF133": 2027,
2030
+ "ZNF207": 2028,
2031
+ "ZNF236": 2029,
2032
+ "ZNF24": 2030,
2033
+ "ZNF253": 2031,
2034
+ "ZNF284": 2032,
2035
+ "ZNF317": 2033,
2036
+ "ZNF335": 2034,
2037
+ "ZNF407": 2035,
2038
+ "ZNF468": 2036,
2039
+ "ZNF492": 2037,
2040
+ "ZNF506": 2038,
2041
+ "ZNF559": 2039,
2042
+ "ZNF574": 2040,
2043
+ "ZNF658": 2041,
2044
+ "ZNF674": 2042,
2045
+ "ZNF676": 2043,
2046
+ "ZNF687": 2044,
2047
+ "ZNF718": 2045,
2048
+ "ZNF720": 2046,
2049
+ "ZNF763": 2047,
2050
+ "ZNF830": 2048,
2051
+ "ZNHIT2": 2049,
2052
+ "ZNHIT3": 2050,
2053
+ "ZNHIT6": 2051,
2054
+ "ZNRD1": 2052,
2055
+ "ZRANB2": 2053,
2056
+ "ZRSR2": 2054,
2057
+ "ZW10": 2055,
2058
+ "ZWINT": 2056
2059
+ }
data/processed/scPerturb/latent_flow_replogle_k562_essential/figure_manifest.txt ADDED
@@ -0,0 +1,12 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/01_split_condition_counts.png
2
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/02_top30_perturbation_gene_counts.png
3
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/03_top_genes_split_composition.png
4
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/04_umi_distribution.png
5
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/05_ngenes_distribution.png
6
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/06_latent_cumulative_explained_variance.png
7
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/07_latent_scatter_by_split.png
8
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/08_latent_scatter_by_condition.png
9
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/09_latent_norm_by_split_condition.png
10
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/10_mean_latent_heatmap_by_split.png
11
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/11_split_gene_count_heatmap_subset.png
12
+ /root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/12_gene_annotation_summary.png
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/01_split_condition_counts.png ADDED
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/02_top30_perturbation_gene_counts.png ADDED

Git LFS Details

  • SHA256: 6bfb535c1b675e9f9ade422cdc9ae34c712153125b876a07b194154851293ca5
  • Pointer size: 131 Bytes
  • Size of remote file: 123 kB
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/03_top_genes_split_composition.png ADDED

Git LFS Details

  • SHA256: 29d31f68cf433e1cd76abf4fee213270e47b9c3ef9119cc3344f6ddfb4b53fd3
  • Pointer size: 131 Bytes
  • Size of remote file: 129 kB
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/04_umi_distribution.png ADDED
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/05_ngenes_distribution.png ADDED
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/06_latent_cumulative_explained_variance.png ADDED
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/07_latent_scatter_by_split.png ADDED

Git LFS Details

  • SHA256: 11c3574dc0e827ad8b63bde7b197882579d1ef936eeb60177680c2cb764b7477
  • Pointer size: 131 Bytes
  • Size of remote file: 727 kB
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/08_latent_scatter_by_condition.png ADDED

Git LFS Details

  • SHA256: 274c0c6829c980ad6607e4e80a908d5da88e0e3c036d7172492672b26175192e
  • Pointer size: 131 Bytes
  • Size of remote file: 599 kB
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/09_latent_norm_by_split_condition.png ADDED
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/10_mean_latent_heatmap_by_split.png ADDED
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/11_split_gene_count_heatmap_subset.png ADDED

Git LFS Details

  • SHA256: 1df94f7d01744ffeabc8ef760aff2d46d5b82fa2581a837e28a6b2887e32dfd9
  • Pointer size: 131 Bytes
  • Size of remote file: 118 kB
data/processed/scPerturb/latent_flow_replogle_k562_essential/figures/12_gene_annotation_summary.png ADDED
data/processed/scPerturb/latent_flow_replogle_k562_essential/flow_indices.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:051043269b16ed696407d5508ee689a0fc8ac6aaeae7827983df92c84c935035
3
+ size 2756594
data/processed/scPerturb/latent_flow_replogle_k562_essential/flow_tensors.pt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:ddfa05df8b306ed62ae143069e95431c635af8ba422bc593e211da2023bf7315
3
+ size 173244239
data/processed/scPerturb/latent_flow_replogle_k562_essential/latent_decoder.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:e5d4740084512a1bd1db2b800aa1dff6f0ce15421ce7de7be95a0adb90abefea
3
+ size 2363221
data/processed/scPerturb/latent_flow_replogle_k562_essential/replogle_k562_essential_latent_flow_ready.h5ad ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:1b2768e5776923cee1742dc9d44c2b5a655bb02e6888e0f4e387485fec9c95e2
3
+ size 2756636608
data/processed/scPerturb/latent_flow_replogle_k562_essential/summary.csv ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ,0
2
+ dataset_name,ReplogleWeissman2022_K562_essential
3
+ n_cells,310385
4
+ n_genes,4334
5
+ d_latent,128
6
+ split_strategy,seen_cell_split
7
+ condition_mode,learnable_id
8
+ n_controls_train,8653
9
+ n_controls_val,1082
10
+ n_controls_test,1081
11
+ n_train_genes,2056
12
+ n_val_genes,2056
13
+ n_test_genes,2056
14
+ explained_variance_ratio_sum,0.12981019914150238
15
+ n_saved_figures,12
16
+ flow_ready_h5ad,/root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/replogle_k562_essential_latent_flow_ready.h5ad
17
+ flow_tensors_pt,/root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/flow_tensors.pt
18
+ flow_indices_pkl,/root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/flow_indices.pkl
19
+ latent_decoder_pkl,/root/final/data/processed/scPerturb/latent_flow_replogle_k562_essential/latent_decoder.pkl
data/processed/scPerturb/prediction_ready/replogle_k562_essential_prediction_ready_summary_full.csv ADDED
@@ -0,0 +1,12 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ,0
2
+ dataset,ReplogleWeissman2022_K562_essential
3
+ n_cells,310385
4
+ n_genes,4334
5
+ n_controls,10816
6
+ n_single_perturbed,299694
7
+ split_counts,"{'train': 248343, 'test': 33235, 'val': 28807}"
8
+ hvg_method,scanpy.seurat_v3 + layer=counts
9
+ hvg_n_top_genes,3000
10
+ n_target_genes_total,2056
11
+ n_target_genes_present,1866
12
+ n_feature_genes,4334
data/processed/scPerturb/prediction_ready/replogle_k562_essential_single_gene_prediction_ready_full.h5ad ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:cee75fff61c44c953b7bb283ce60bef220424383fb80cd0779d5ada0d714d9ee
3
+ size 2460410638
src/data/latent_space.ipynb CHANGED
@@ -36,16 +36,448 @@
36
  },
37
  {
38
  "cell_type": "code",
39
- "execution_count": 2,
40
  "id": "setup",
41
  "metadata": {},
42
  "outputs": [
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
43
  {
44
  "name": "stderr",
45
  "output_type": "stream",
46
  "text": [
47
- "/opt/miniconda3/lib/python3.13/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
48
- " from .autonotebook import tqdm as notebook_tqdm\n",
49
  "Seed set to 7\n"
50
  ]
51
  },
@@ -53,22 +485,30 @@
53
  "name": "stdout",
54
  "output_type": "stream",
55
  "text": [
56
- "Kernel python: /opt/miniconda3/bin/python\n",
57
- "Project root: /Users/yurujiang/Desktop/final_thesis\n",
58
- "Data root: /Users/yurujiang/Desktop/final_thesis/data/scPerturb\n",
59
- "Metadata path: /Users/yurujiang/Desktop/final_thesis/data/processed/scPerturb/cell_metadata_standardized.csv\n",
60
- "Output dir: /Users/yurujiang/Desktop/final_thesis/data/processed/scPerturb/latent_space\n",
61
- "Figure dir: /Users/yurujiang/Desktop/final_thesis/data/processed/scPerturb/latent_space/figures\n",
62
  "scanpy version: 1.12\n",
63
  "scvi-tools version: 1.4.2\n",
64
- "torch version: 2.7.1\n",
65
- "torch.cuda.is_available: False\n",
66
- "torch.backends.mps.is_available: True\n",
67
- "SCVI accelerator/devices: mps/1\n"
68
  ]
69
  }
70
  ],
71
  "source": [
 
 
 
 
 
 
 
 
72
  "from __future__ import annotations\n",
73
  "\n",
74
  "from pathlib import Path\n",
@@ -168,7 +608,7 @@
168
  },
169
  {
170
  "cell_type": "code",
171
- "execution_count": 3,
172
  "id": "metadata-selection",
173
  "metadata": {},
174
  "outputs": [
@@ -251,7 +691,7 @@
251
  "0 0.002774 [CRISPR] "
252
  ]
253
  },
254
- "execution_count": 3,
255
  "metadata": {},
256
  "output_type": "execute_result"
257
  }
@@ -304,7 +744,7 @@
304
  },
305
  {
306
  "cell_type": "code",
307
- "execution_count": 4,
308
  "id": "helpers",
309
  "metadata": {},
310
  "outputs": [],
@@ -413,7 +853,7 @@
413
  },
414
  {
415
  "cell_type": "code",
416
- "execution_count": 5,
417
  "id": "gene-space-build",
418
  "metadata": {},
419
  "outputs": [
@@ -510,7 +950,7 @@
510
  "ENSG00000187608 ENSG00000187608 2946.0 2180 ISG15"
511
  ]
512
  },
513
- "execution_count": 5,
514
  "metadata": {},
515
  "output_type": "execute_result"
516
  }
@@ -1228,7 +1668,7 @@
1228
  },
1229
  {
1230
  "cell_type": "code",
1231
- "execution_count": null,
1232
  "id": "36db668b",
1233
  "metadata": {},
1234
  "outputs": [
@@ -1237,7 +1677,7 @@
1237
  "output_type": "stream",
1238
  "text": [
1239
  "[Step 1/11] Read dataset file\n",
1240
- "Reading dataset: /Users/yurujiang/Desktop/final_thesis/data/scPerturb/rna_protein/ReplogleWeissman2022_K562_essential.h5ad\n",
1241
  "[FULL_RUN] Loaded full adata: n_obs=310385, n_vars=8563\n",
1242
  "[Step 2/11] Identify key metadata columns\n",
1243
  "obs columns count: 24\n",
@@ -1254,7 +1694,37 @@
1254
  "[FULL_RUN] Using all filtered cells: 310385\n",
1255
  "[Step 6/11] Normalize and log-transform expression\n",
1256
  "post-log1p matrix shape: (310385, 8563)\n",
1257
- "[Step 7/11] Select HVGs\n"
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1258
  ]
1259
  }
1260
  ],
@@ -1539,7 +2009,7 @@
1539
  ],
1540
  "metadata": {
1541
  "kernelspec": {
1542
- "display_name": "base",
1543
  "language": "python",
1544
  "name": "python3"
1545
  },
@@ -1553,7 +2023,7 @@
1553
  "name": "python",
1554
  "nbconvert_exporter": "python",
1555
  "pygments_lexer": "ipython3",
1556
- "version": "3.13.5"
1557
  }
1558
  },
1559
  "nbformat": 4,
 
36
  },
37
  {
38
  "cell_type": "code",
39
+ "execution_count": 1,
40
  "id": "setup",
41
  "metadata": {},
42
  "outputs": [
43
+ {
44
+ "name": "stdout",
45
+ "output_type": "stream",
46
+ "text": [
47
+ "Collecting scanpy\n",
48
+ " Downloading scanpy-1.12-py3-none-any.whl.metadata (8.4 kB)\n",
49
+ "Collecting anndata>=0.10.8 (from scanpy)\n",
50
+ " Downloading anndata-0.12.10-py3-none-any.whl.metadata (9.9 kB)\n",
51
+ "Collecting fast-array-utils>=1.2.1 (from fast-array-utils[accel,sparse]>=1.2.1->scanpy)\n",
52
+ " Downloading fast_array_utils-1.4-py3-none-any.whl.metadata (2.7 kB)\n",
53
+ "Collecting h5py>=3.11 (from scanpy)\n",
54
+ " Downloading h5py-3.16.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (3.0 kB)\n",
55
+ "Collecting joblib (from scanpy)\n",
56
+ " Downloading joblib-1.5.3-py3-none-any.whl.metadata (5.5 kB)\n",
57
+ "Collecting legacy-api-wrap>=1.5 (from scanpy)\n",
58
+ " Downloading legacy_api_wrap-1.5-py3-none-any.whl.metadata (2.2 kB)\n",
59
+ "Collecting matplotlib>=3.9 (from scanpy)\n",
60
+ " Downloading matplotlib-3.10.8-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (52 kB)\n",
61
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m52.8/52.8 kB\u001b[0m \u001b[31m969.5 kB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m \u001b[36m0:00:01\u001b[0m\n",
62
+ "\u001b[?25hCollecting natsort (from scanpy)\n",
63
+ " Downloading natsort-8.4.0-py3-none-any.whl.metadata (21 kB)\n",
64
+ "Collecting networkx>=2.8.8 (from scanpy)\n",
65
+ " Downloading networkx-3.6.1-py3-none-any.whl.metadata (6.8 kB)\n",
66
+ "Collecting numba>=0.60 (from scanpy)\n",
67
+ " Downloading numba-0.65.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.9 kB)\n",
68
+ "Requirement already satisfied: numpy>=2 in /usr/local/lib/python3.12/dist-packages (from scanpy) (2.4.3)\n",
69
+ "Requirement already satisfied: packaging>=25 in /usr/local/lib/python3.12/dist-packages (from scanpy) (26.0)\n",
70
+ "Collecting pandas>=2.2.2 (from scanpy)\n",
71
+ " Downloading pandas-3.0.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)\n",
72
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m79.5/79.5 kB\u001b[0m \u001b[31m2.5 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
73
+ "\u001b[?25hCollecting patsy (from scanpy)\n",
74
+ " Downloading patsy-1.0.2-py2.py3-none-any.whl.metadata (3.6 kB)\n",
75
+ "Collecting pynndescent>=0.5.13 (from scanpy)\n",
76
+ " Downloading pynndescent-0.6.0-py3-none-any.whl.metadata (6.9 kB)\n",
77
+ "Collecting scikit-learn>=1.4.2 (from scanpy)\n",
78
+ " Downloading scikit_learn-1.8.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (11 kB)\n",
79
+ "Collecting scipy>=1.13 (from scanpy)\n",
80
+ " Downloading scipy-1.17.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)\n",
81
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m62.1/62.1 kB\u001b[0m \u001b[31m3.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
82
+ "\u001b[?25hCollecting seaborn>=0.13.2 (from scanpy)\n",
83
+ " Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)\n",
84
+ "Collecting session-info2 (from scanpy)\n",
85
+ " Downloading session_info2-0.4-py3-none-any.whl.metadata (3.5 kB)\n",
86
+ "Collecting statsmodels>=0.14.5 (from scanpy)\n",
87
+ " Downloading statsmodels-0.14.6-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (9.5 kB)\n",
88
+ "Requirement already satisfied: tqdm in /usr/local/lib/python3.12/dist-packages (from scanpy) (4.67.3)\n",
89
+ "Requirement already satisfied: typing-extensions in /usr/local/lib/python3.12/dist-packages (from scanpy) (4.15.0)\n",
90
+ "Collecting umap-learn>=0.5.7 (from scanpy)\n",
91
+ " Downloading umap_learn-0.5.11-py3-none-any.whl.metadata (26 kB)\n",
92
+ "Collecting array-api-compat>=1.7.1 (from anndata>=0.10.8->scanpy)\n",
93
+ " Downloading array_api_compat-1.14.0-py3-none-any.whl.metadata (2.5 kB)\n",
94
+ "Collecting pandas>=2.2.2 (from scanpy)\n",
95
+ " Downloading pandas-2.3.3-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)\n",
96
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m91.2/91.2 kB\u001b[0m \u001b[31m3.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
97
+ "\u001b[?25hCollecting zarr!=3.0.*,>=2.18.7 (from anndata>=0.10.8->scanpy)\n",
98
+ " Downloading zarr-3.1.6-py3-none-any.whl.metadata (8.6 kB)\n",
99
+ "Collecting contourpy>=1.0.1 (from matplotlib>=3.9->scanpy)\n",
100
+ " Downloading contourpy-1.3.3-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (5.5 kB)\n",
101
+ "Collecting cycler>=0.10 (from matplotlib>=3.9->scanpy)\n",
102
+ " Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)\n",
103
+ "Collecting fonttools>=4.22.0 (from matplotlib>=3.9->scanpy)\n",
104
+ " Downloading fonttools-4.62.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (117 kB)\n",
105
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m117.5/117.5 kB\u001b[0m \u001b[31m4.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
106
+ "\u001b[?25hCollecting kiwisolver>=1.3.1 (from matplotlib>=3.9->scanpy)\n",
107
+ " Downloading kiwisolver-1.5.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (5.1 kB)\n",
108
+ "Requirement already satisfied: pillow>=8 in /usr/local/lib/python3.12/dist-packages (from matplotlib>=3.9->scanpy) (12.1.1)\n",
109
+ "Requirement already satisfied: pyparsing>=3 in /usr/lib/python3/dist-packages (from matplotlib>=3.9->scanpy) (3.1.1)\n",
110
+ "Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.12/dist-packages (from matplotlib>=3.9->scanpy) (2.9.0.post0)\n",
111
+ "Collecting llvmlite<0.48,>=0.47.0dev0 (from numba>=0.60->scanpy)\n",
112
+ " Downloading llvmlite-0.47.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (5.0 kB)\n",
113
+ "Collecting pytz>=2020.1 (from pandas>=2.2.2->scanpy)\n",
114
+ " Downloading pytz-2026.1.post1-py2.py3-none-any.whl.metadata (22 kB)\n",
115
+ "Requirement already satisfied: tzdata>=2022.7 in /usr/local/lib/python3.12/dist-packages (from pandas>=2.2.2->scanpy) (2025.3)\n",
116
+ "Collecting threadpoolctl>=3.2.0 (from scikit-learn>=1.4.2->scanpy)\n",
117
+ " Downloading threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)\n",
118
+ "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.12/dist-packages (from python-dateutil>=2.7->matplotlib>=3.9->scanpy) (1.17.0)\n",
119
+ "Collecting donfig>=0.8 (from zarr!=3.0.*,>=2.18.7->anndata>=0.10.8->scanpy)\n",
120
+ " Downloading donfig-0.8.1.post1-py3-none-any.whl.metadata (5.0 kB)\n",
121
+ "Collecting google-crc32c>=1.5 (from zarr!=3.0.*,>=2.18.7->anndata>=0.10.8->scanpy)\n",
122
+ " Downloading google_crc32c-1.8.0-cp312-cp312-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl.metadata (1.7 kB)\n",
123
+ "Collecting numcodecs>=0.14 (from zarr!=3.0.*,>=2.18.7->anndata>=0.10.8->scanpy)\n",
124
+ " Downloading numcodecs-0.16.5-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (3.4 kB)\n",
125
+ "Requirement already satisfied: pyyaml in /usr/local/lib/python3.12/dist-packages (from donfig>=0.8->zarr!=3.0.*,>=2.18.7->anndata>=0.10.8->scanpy) (6.0.3)\n",
126
+ "Downloading scanpy-1.12-py3-none-any.whl (2.1 MB)\n",
127
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m2.1/2.1 MB\u001b[0m \u001b[31m14.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
128
+ "\u001b[?25hDownloading anndata-0.12.10-py3-none-any.whl (176 kB)\n",
129
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m176.6/176.6 kB\u001b[0m \u001b[31m52.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
130
+ "\u001b[?25hDownloading fast_array_utils-1.4-py3-none-any.whl (38 kB)\n",
131
+ "Downloading h5py-3.16.0-cp312-cp312-manylinux_2_28_x86_64.whl (5.4 MB)\n",
132
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m5.4/5.4 MB\u001b[0m \u001b[31m52.5 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0mm\n",
133
+ "\u001b[?25hDownloading legacy_api_wrap-1.5-py3-none-any.whl (10 kB)\n",
134
+ "Downloading matplotlib-3.10.8-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (8.7 MB)\n",
135
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m8.7/8.7 MB\u001b[0m \u001b[31m72.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0ma \u001b[36m0:00:01\u001b[0m\n",
136
+ "\u001b[?25hDownloading networkx-3.6.1-py3-none-any.whl (2.1 MB)\n",
137
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m2.1/2.1 MB\u001b[0m \u001b[31m79.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
138
+ "\u001b[?25hDownloading numba-0.65.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.8 MB)\n",
139
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m3.8/3.8 MB\u001b[0m \u001b[31m74.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0mta \u001b[36m0:00:01\u001b[0m\n",
140
+ "\u001b[?25hDownloading pandas-2.3.3-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (12.4 MB)\n",
141
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m12.4/12.4 MB\u001b[0m \u001b[31m77.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m0:01\u001b[0m\n",
142
+ "\u001b[?25hDownloading pynndescent-0.6.0-py3-none-any.whl (73 kB)\n",
143
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m73.5/73.5 kB\u001b[0m \u001b[31m11.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
144
+ "\u001b[?25hDownloading joblib-1.5.3-py3-none-any.whl (309 kB)\n",
145
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m309.1/309.1 kB\u001b[0m \u001b[31m39.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
146
+ "\u001b[?25hDownloading scikit_learn-1.8.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (8.9 MB)\n",
147
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m8.9/8.9 MB\u001b[0m \u001b[31m87.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0ma \u001b[36m0:00:01\u001b[0mm\n",
148
+ "\u001b[?25hDownloading scipy-1.17.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (35.2 MB)\n",
149
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m35.2/35.2 MB\u001b[0m \u001b[31m65.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
150
+ "\u001b[?25hDownloading seaborn-0.13.2-py3-none-any.whl (294 kB)\n",
151
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m294.9/294.9 kB\u001b[0m \u001b[31m37.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
152
+ "\u001b[?25hDownloading statsmodels-0.14.6-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (10.3 MB)\n",
153
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m10.3/10.3 MB\u001b[0m \u001b[31m79.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m0:01\u001b[0mm\n",
154
+ "\u001b[?25hDownloading patsy-1.0.2-py2.py3-none-any.whl (233 kB)\n",
155
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m233.3/233.3 kB\u001b[0m \u001b[31m32.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
156
+ "\u001b[?25hDownloading umap_learn-0.5.11-py3-none-any.whl (90 kB)\n",
157
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m90.9/90.9 kB\u001b[0m \u001b[31m15.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
158
+ "\u001b[?25hDownloading natsort-8.4.0-py3-none-any.whl (38 kB)\n",
159
+ "Downloading session_info2-0.4-py3-none-any.whl (17 kB)\n",
160
+ "Downloading array_api_compat-1.14.0-py3-none-any.whl (60 kB)\n",
161
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m60.1/60.1 kB\u001b[0m \u001b[31m18.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
162
+ "\u001b[?25hDownloading contourpy-1.3.3-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (362 kB)\n",
163
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m362.6/362.6 kB\u001b[0m \u001b[31m57.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
164
+ "\u001b[?25hDownloading cycler-0.12.1-py3-none-any.whl (8.3 kB)\n",
165
+ "Downloading fonttools-4.62.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (5.0 MB)\n",
166
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m5.0/5.0 MB\u001b[0m \u001b[31m54.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0ma \u001b[36m0:00:01\u001b[0mm\n",
167
+ "\u001b[?25hDownloading kiwisolver-1.5.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.5 MB)\n",
168
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m1.5/1.5 MB\u001b[0m \u001b[31m83.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
169
+ "\u001b[?25hDownloading llvmlite-0.47.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (56.3 MB)\n",
170
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m56.3/56.3 MB\u001b[0m \u001b[31m59.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
171
+ "\u001b[?25hDownloading pytz-2026.1.post1-py2.py3-none-any.whl (510 kB)\n",
172
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m510.5/510.5 kB\u001b[0m \u001b[31m62.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
173
+ "\u001b[?25hDownloading threadpoolctl-3.6.0-py3-none-any.whl (18 kB)\n",
174
+ "Downloading zarr-3.1.6-py3-none-any.whl (295 kB)\n",
175
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m295.7/295.7 kB\u001b[0m \u001b[31m80.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
176
+ "\u001b[?25hDownloading donfig-0.8.1.post1-py3-none-any.whl (21 kB)\n",
177
+ "Downloading google_crc32c-1.8.0-cp312-cp312-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl (33 kB)\n",
178
+ "Downloading numcodecs-0.16.5-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (9.2 MB)\n",
179
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m9.2/9.2 MB\u001b[0m \u001b[31m87.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
180
+ "\u001b[?25hInstalling collected packages: pytz, threadpoolctl, session-info2, scipy, patsy, numcodecs, networkx, natsort, llvmlite, legacy-api-wrap, kiwisolver, joblib, h5py, google-crc32c, fonttools, fast-array-utils, donfig, cycler, contourpy, array-api-compat, zarr, scikit-learn, pandas, numba, matplotlib, statsmodels, seaborn, pynndescent, anndata, umap-learn, scanpy\n",
181
+ "Successfully installed anndata-0.12.10 array-api-compat-1.14.0 contourpy-1.3.3 cycler-0.12.1 donfig-0.8.1.post1 fast-array-utils-1.4 fonttools-4.62.1 google-crc32c-1.8.0 h5py-3.16.0 joblib-1.5.3 kiwisolver-1.5.0 legacy-api-wrap-1.5 llvmlite-0.47.0 matplotlib-3.10.8 natsort-8.4.0 networkx-3.6.1 numba-0.65.0 numcodecs-0.16.5 pandas-2.3.3 patsy-1.0.2 pynndescent-0.6.0 pytz-2026.1.post1 scanpy-1.12 scikit-learn-1.8.0 scipy-1.17.1 seaborn-0.13.2 session-info2-0.4 statsmodels-0.14.6 threadpoolctl-3.6.0 umap-learn-0.5.11 zarr-3.1.6\n",
182
+ "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n",
183
+ "\u001b[0mCollecting scvi-tools\n",
184
+ " Downloading scvi_tools-1.4.2-py3-none-any.whl.metadata (23 kB)\n",
185
+ "Requirement already satisfied: anndata in /usr/local/lib/python3.12/dist-packages (from scvi-tools) (0.12.10)\n",
186
+ "Collecting docrep>=0.3.2 (from scvi-tools)\n",
187
+ " Downloading docrep-0.3.2.tar.gz (33 kB)\n",
188
+ " Preparing metadata (setup.py) ... \u001b[?25ldone\n",
189
+ "\u001b[?25hCollecting lightning>=2.0 (from scvi-tools)\n",
190
+ " Downloading lightning-2.6.1-py3-none-any.whl.metadata (44 kB)\n",
191
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m44.8/44.8 kB\u001b[0m \u001b[31m1.5 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
192
+ "\u001b[?25hCollecting ml-collections (from scvi-tools)\n",
193
+ " Downloading ml_collections-1.1.0-py3-none-any.whl.metadata (22 kB)\n",
194
+ "Collecting mudata (from scvi-tools)\n",
195
+ " Downloading mudata-0.3.3-py3-none-any.whl.metadata (10 kB)\n",
196
+ "Requirement already satisfied: numba>=0.60.0 in /usr/local/lib/python3.12/dist-packages (from scvi-tools) (0.65.0)\n",
197
+ "Requirement already satisfied: numpy in /usr/local/lib/python3.12/dist-packages (from scvi-tools) (2.4.3)\n",
198
+ "Requirement already satisfied: pandas in /usr/local/lib/python3.12/dist-packages (from scvi-tools) (2.3.3)\n",
199
+ "Collecting pyro-ppl (from scvi-tools)\n",
200
+ " Downloading pyro_ppl-1.9.1-py3-none-any.whl.metadata (7.8 kB)\n",
201
+ "Collecting rich (from scvi-tools)\n",
202
+ " Downloading rich-14.3.3-py3-none-any.whl.metadata (18 kB)\n",
203
+ "Requirement already satisfied: scanpy>=1.10 in /usr/local/lib/python3.12/dist-packages (from scanpy[skmisc]>=1.10->scvi-tools) (1.12)\n",
204
+ "Requirement already satisfied: scikit-learn in /usr/local/lib/python3.12/dist-packages (from scvi-tools) (1.8.0)\n",
205
+ "Requirement already satisfied: scipy in /usr/local/lib/python3.12/dist-packages (from scvi-tools) (1.17.1)\n",
206
+ "Collecting sparse>=0.14.0 (from scvi-tools)\n",
207
+ " Downloading sparse-0.18.0-py2.py3-none-any.whl.metadata (5.3 kB)\n",
208
+ "Requirement already satisfied: tensorboard in /usr/local/lib/python3.12/dist-packages (from scvi-tools) (2.20.0)\n",
209
+ "Collecting torch (from scvi-tools)\n",
210
+ " Downloading torch-2.11.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (29 kB)\n",
211
+ "Collecting torchmetrics (from scvi-tools)\n",
212
+ " Downloading torchmetrics-1.9.0-py3-none-any.whl.metadata (23 kB)\n",
213
+ "Requirement already satisfied: tqdm in /usr/local/lib/python3.12/dist-packages (from scvi-tools) (4.67.3)\n",
214
+ "Collecting xarray (from scvi-tools)\n",
215
+ " Downloading xarray-2026.2.0-py3-none-any.whl.metadata (12 kB)\n",
216
+ "Requirement already satisfied: six in /usr/local/lib/python3.12/dist-packages (from docrep>=0.3.2->scvi-tools) (1.17.0)\n",
217
+ "Requirement already satisfied: PyYAML<8.0,>5.4 in /usr/local/lib/python3.12/dist-packages (from lightning>=2.0->scvi-tools) (6.0.3)\n",
218
+ "Collecting fsspec<2028.0,>=2022.5.0 (from fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools)\n",
219
+ " Downloading fsspec-2026.3.0-py3-none-any.whl.metadata (10 kB)\n",
220
+ "Collecting lightning-utilities<2.0,>=0.10.0 (from lightning>=2.0->scvi-tools)\n",
221
+ " Downloading lightning_utilities-0.15.3-py3-none-any.whl.metadata (5.5 kB)\n",
222
+ "Requirement already satisfied: packaging<27.0,>=23.0 in /usr/local/lib/python3.12/dist-packages (from lightning>=2.0->scvi-tools) (26.0)\n",
223
+ "Requirement already satisfied: typing-extensions<6.0,>4.5.0 in /usr/local/lib/python3.12/dist-packages (from lightning>=2.0->scvi-tools) (4.15.0)\n",
224
+ "Collecting pytorch-lightning (from lightning>=2.0->scvi-tools)\n",
225
+ " Downloading pytorch_lightning-2.6.1-py3-none-any.whl.metadata (21 kB)\n",
226
+ "Requirement already satisfied: llvmlite<0.48,>=0.47.0dev0 in /usr/local/lib/python3.12/dist-packages (from numba>=0.60.0->scvi-tools) (0.47.0)\n",
227
+ "Requirement already satisfied: fast-array-utils>=1.2.1 in /usr/local/lib/python3.12/dist-packages (from fast-array-utils[accel,sparse]>=1.2.1->scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (1.4)\n",
228
+ "Requirement already satisfied: h5py>=3.11 in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (3.16.0)\n",
229
+ "Requirement already satisfied: joblib in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (1.5.3)\n",
230
+ "Requirement already satisfied: legacy-api-wrap>=1.5 in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (1.5)\n",
231
+ "Requirement already satisfied: matplotlib>=3.9 in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (3.10.8)\n",
232
+ "Requirement already satisfied: natsort in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (8.4.0)\n",
233
+ "Requirement already satisfied: networkx>=2.8.8 in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (3.6.1)\n",
234
+ "Requirement already satisfied: patsy in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (1.0.2)\n",
235
+ "Requirement already satisfied: pynndescent>=0.5.13 in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (0.6.0)\n",
236
+ "Requirement already satisfied: seaborn>=0.13.2 in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (0.13.2)\n",
237
+ "Requirement already satisfied: session-info2 in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (0.4)\n",
238
+ "Requirement already satisfied: statsmodels>=0.14.5 in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (0.14.6)\n",
239
+ "Requirement already satisfied: umap-learn>=0.5.7 in /usr/local/lib/python3.12/dist-packages (from scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (0.5.11)\n",
240
+ "Requirement already satisfied: array-api-compat>=1.7.1 in /usr/local/lib/python3.12/dist-packages (from anndata->scvi-tools) (1.14.0)\n",
241
+ "Requirement already satisfied: zarr!=3.0.*,>=2.18.7 in /usr/local/lib/python3.12/dist-packages (from anndata->scvi-tools) (3.1.6)\n",
242
+ "Requirement already satisfied: python-dateutil>=2.8.2 in /usr/local/lib/python3.12/dist-packages (from pandas->scvi-tools) (2.9.0.post0)\n",
243
+ "Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.12/dist-packages (from pandas->scvi-tools) (2026.1.post1)\n",
244
+ "Requirement already satisfied: tzdata>=2022.7 in /usr/local/lib/python3.12/dist-packages (from pandas->scvi-tools) (2025.3)\n",
245
+ "Collecting scikit-misc>=0.5.1 (from scanpy[skmisc]>=1.10->scvi-tools)\n",
246
+ " Downloading scikit_misc-0.5.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (5.0 kB)\n",
247
+ "Requirement already satisfied: threadpoolctl>=3.2.0 in /usr/local/lib/python3.12/dist-packages (from scikit-learn->scvi-tools) (3.6.0)\n",
248
+ "Collecting filelock (from torch->scvi-tools)\n",
249
+ " Downloading filelock-3.25.2-py3-none-any.whl.metadata (2.0 kB)\n",
250
+ "Collecting setuptools<82 (from torch->scvi-tools)\n",
251
+ " Downloading setuptools-81.0.0-py3-none-any.whl.metadata (6.6 kB)\n",
252
+ "Collecting sympy>=1.13.3 (from torch->scvi-tools)\n",
253
+ " Downloading sympy-1.14.0-py3-none-any.whl.metadata (12 kB)\n",
254
+ "Requirement already satisfied: jinja2 in /usr/local/lib/python3.12/dist-packages (from torch->scvi-tools) (3.1.6)\n",
255
+ "Collecting cuda-toolkit==13.0.2 (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
256
+ " Downloading cuda_toolkit-13.0.2-py2.py3-none-any.whl.metadata (9.4 kB)\n",
257
+ "Collecting cuda-bindings<14,>=13.0.3 (from torch->scvi-tools)\n",
258
+ " Downloading cuda_bindings-13.2.0-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (2.3 kB)\n",
259
+ "Collecting nvidia-cudnn-cu13==9.19.0.56 (from torch->scvi-tools)\n",
260
+ " Downloading nvidia_cudnn_cu13-9.19.0.56-py3-none-manylinux_2_27_x86_64.whl.metadata (1.9 kB)\n",
261
+ "Collecting nvidia-cusparselt-cu13==0.8.0 (from torch->scvi-tools)\n",
262
+ " Downloading nvidia_cusparselt_cu13-0.8.0-py3-none-manylinux2014_x86_64.whl.metadata (12 kB)\n",
263
+ "Collecting nvidia-nccl-cu13==2.28.9 (from torch->scvi-tools)\n",
264
+ " Downloading nvidia_nccl_cu13-2.28.9-py3-none-manylinux_2_18_x86_64.whl.metadata (2.0 kB)\n",
265
+ "Collecting nvidia-nvshmem-cu13==3.4.5 (from torch->scvi-tools)\n",
266
+ " Downloading nvidia_nvshmem_cu13-3.4.5-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.1 kB)\n",
267
+ "Collecting triton==3.6.0 (from torch->scvi-tools)\n",
268
+ " Downloading triton-3.6.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.7 kB)\n",
269
+ "Collecting nvidia-cublas==13.1.0.3.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
270
+ " Downloading nvidia_cublas-13.1.0.3-py3-none-manylinux_2_27_x86_64.whl.metadata (1.7 kB)\n",
271
+ "Collecting nvidia-cuda-runtime==13.0.96.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
272
+ " Downloading nvidia_cuda_runtime-13.0.96-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.7 kB)\n",
273
+ "Collecting nvidia-cufft==12.0.0.61.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
274
+ " Downloading nvidia_cufft-12.0.0.61-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.8 kB)\n",
275
+ "Collecting nvidia-cufile==1.15.1.6.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
276
+ " Downloading nvidia_cufile-1.15.1.6-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.7 kB)\n",
277
+ "Collecting nvidia-cuda-cupti==13.0.85.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
278
+ " Downloading nvidia_cuda_cupti-13.0.85-py3-none-manylinux_2_25_x86_64.whl.metadata (1.7 kB)\n",
279
+ "Collecting nvidia-curand==10.4.0.35.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
280
+ " Downloading nvidia_curand-10.4.0.35-py3-none-manylinux_2_27_x86_64.whl.metadata (1.7 kB)\n",
281
+ "Collecting nvidia-cusolver==12.0.4.66.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
282
+ " Downloading nvidia_cusolver-12.0.4.66-py3-none-manylinux_2_27_x86_64.whl.metadata (1.8 kB)\n",
283
+ "Collecting nvidia-cusparse==12.6.3.3.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
284
+ " Downloading nvidia_cusparse-12.6.3.3-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.8 kB)\n",
285
+ "Collecting nvidia-nvjitlink==13.0.88.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
286
+ " Downloading nvidia_nvjitlink-13.0.88-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl.metadata (1.7 kB)\n",
287
+ "Collecting nvidia-cuda-nvrtc==13.0.88.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
288
+ " Downloading nvidia_cuda_nvrtc-13.0.88-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl.metadata (1.7 kB)\n",
289
+ "Collecting nvidia-nvtx==13.0.85.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == \"Linux\"->torch->scvi-tools)\n",
290
+ " Downloading nvidia_nvtx-13.0.85-py3-none-manylinux1_x86_64.manylinux_2_5_x86_64.whl.metadata (1.8 kB)\n",
291
+ "Requirement already satisfied: absl-py in /usr/local/lib/python3.12/dist-packages (from ml-collections->scvi-tools) (2.4.0)\n",
292
+ "Collecting opt-einsum>=2.3.2 (from pyro-ppl->scvi-tools)\n",
293
+ " Downloading opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB)\n",
294
+ "Collecting pyro-api>=0.1.1 (from pyro-ppl->scvi-tools)\n",
295
+ " Downloading pyro_api-0.1.2-py3-none-any.whl.metadata (2.5 kB)\n",
296
+ "Collecting markdown-it-py>=2.2.0 (from rich->scvi-tools)\n",
297
+ " Downloading markdown_it_py-4.0.0-py3-none-any.whl.metadata (7.3 kB)\n",
298
+ "Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /usr/local/lib/python3.12/dist-packages (from rich->scvi-tools) (2.19.2)\n",
299
+ "Requirement already satisfied: grpcio>=1.48.2 in /usr/local/lib/python3.12/dist-packages (from tensorboard->scvi-tools) (1.78.0)\n",
300
+ "Requirement already satisfied: markdown>=2.6.8 in /usr/local/lib/python3.12/dist-packages (from tensorboard->scvi-tools) (3.10.2)\n",
301
+ "Requirement already satisfied: pillow in /usr/local/lib/python3.12/dist-packages (from tensorboard->scvi-tools) (12.1.1)\n",
302
+ "Requirement already satisfied: protobuf!=4.24.0,>=3.19.6 in /usr/local/lib/python3.12/dist-packages (from tensorboard->scvi-tools) (7.34.0)\n",
303
+ "Requirement already satisfied: tensorboard-data-server<0.8.0,>=0.7.0 in /usr/local/lib/python3.12/dist-packages (from tensorboard->scvi-tools) (0.7.2)\n",
304
+ "Requirement already satisfied: werkzeug>=1.0.1 in /usr/local/lib/python3.12/dist-packages (from tensorboard->scvi-tools) (3.1.6)\n",
305
+ "Collecting cuda-pathfinder~=1.1 (from cuda-bindings<14,>=13.0.3->torch->scvi-tools)\n",
306
+ " Downloading cuda_pathfinder-1.5.2-py3-none-any.whl.metadata (1.9 kB)\n",
307
+ "Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools)\n",
308
+ " Downloading aiohttp-3.13.5-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB)\n",
309
+ "Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich->scvi-tools)\n",
310
+ " Downloading mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)\n",
311
+ "Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.12/dist-packages (from matplotlib>=3.9->scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (1.3.3)\n",
312
+ "Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.12/dist-packages (from matplotlib>=3.9->scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (0.12.1)\n",
313
+ "Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.12/dist-packages (from matplotlib>=3.9->scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (4.62.1)\n",
314
+ "Requirement already satisfied: kiwisolver>=1.3.1 in /usr/local/lib/python3.12/dist-packages (from matplotlib>=3.9->scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (1.5.0)\n",
315
+ "Requirement already satisfied: pyparsing>=3 in /usr/lib/python3/dist-packages (from matplotlib>=3.9->scanpy>=1.10->scanpy[skmisc]>=1.10->scvi-tools) (3.1.1)\n",
316
+ "Collecting mpmath<1.4,>=1.1.0 (from sympy>=1.13.3->torch->scvi-tools)\n",
317
+ " Downloading mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)\n",
318
+ "Requirement already satisfied: markupsafe>=2.1.1 in /usr/local/lib/python3.12/dist-packages (from werkzeug>=1.0.1->tensorboard->scvi-tools) (3.0.3)\n",
319
+ "Requirement already satisfied: donfig>=0.8 in /usr/local/lib/python3.12/dist-packages (from zarr!=3.0.*,>=2.18.7->anndata->scvi-tools) (0.8.1.post1)\n",
320
+ "Requirement already satisfied: google-crc32c>=1.5 in /usr/local/lib/python3.12/dist-packages (from zarr!=3.0.*,>=2.18.7->anndata->scvi-tools) (1.8.0)\n",
321
+ "Requirement already satisfied: numcodecs>=0.14 in /usr/local/lib/python3.12/dist-packages (from zarr!=3.0.*,>=2.18.7->anndata->scvi-tools) (0.16.5)\n",
322
+ "Collecting aiohappyeyeballs>=2.5.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools)\n",
323
+ " Downloading aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB)\n",
324
+ "Collecting aiosignal>=1.4.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools)\n",
325
+ " Downloading aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)\n",
326
+ "Requirement already satisfied: attrs>=17.3.0 in /usr/local/lib/python3.12/dist-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools) (25.4.0)\n",
327
+ "Collecting frozenlist>=1.1.1 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools)\n",
328
+ " Downloading frozenlist-1.8.0-cp312-cp312-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (20 kB)\n",
329
+ "Collecting multidict<7.0,>=4.5 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools)\n",
330
+ " Downloading multidict-6.7.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB)\n",
331
+ "Collecting propcache>=0.2.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools)\n",
332
+ " Downloading propcache-0.4.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (13 kB)\n",
333
+ "Collecting yarl<2.0,>=1.17.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools)\n",
334
+ " Downloading yarl-1.23.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)\n",
335
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m79.6/79.6 kB\u001b[0m \u001b[31m1.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0ma \u001b[36m0:00:01\u001b[0m\n",
336
+ "\u001b[?25hRequirement already satisfied: idna>=2.0 in /usr/local/lib/python3.12/dist-packages (from yarl<2.0,>=1.17.0->aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools) (3.11)\n",
337
+ "Downloading scvi_tools-1.4.2-py3-none-any.whl (662 kB)\n",
338
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m662.1/662.1 kB\u001b[0m \u001b[31m5.5 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0ma \u001b[36m0:00:01\u001b[0m\n",
339
+ "\u001b[?25hDownloading lightning-2.6.1-py3-none-any.whl (853 kB)\n",
340
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m853.6/853.6 kB\u001b[0m \u001b[31m17.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0ma \u001b[36m0:00:01\u001b[0m\n",
341
+ "\u001b[?25hDownloading sparse-0.18.0-py2.py3-none-any.whl (151 kB)\n",
342
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m151.9/151.9 kB\u001b[0m \u001b[31m22.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
343
+ "\u001b[?25hDownloading torch-2.11.0-cp312-cp312-manylinux_2_28_x86_64.whl (530.7 MB)\n",
344
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m530.7/530.7 MB\u001b[0m \u001b[31m18.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
345
+ "\u001b[?25hDownloading cuda_toolkit-13.0.2-py2.py3-none-any.whl (2.4 kB)\n",
346
+ "Downloading nvidia_cudnn_cu13-9.19.0.56-py3-none-manylinux_2_27_x86_64.whl (366.1 MB)\n",
347
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m366.1/366.1 MB\u001b[0m \u001b[31m23.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
348
+ "\u001b[?25hDownloading nvidia_cusparselt_cu13-0.8.0-py3-none-manylinux2014_x86_64.whl (169.9 MB)\n",
349
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m169.9/169.9 MB\u001b[0m \u001b[31m38.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
350
+ "\u001b[?25hDownloading nvidia_nccl_cu13-2.28.9-py3-none-manylinux_2_18_x86_64.whl (196.5 MB)\n",
351
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m196.5/196.5 MB\u001b[0m \u001b[31m32.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
352
+ "\u001b[?25hDownloading nvidia_nvshmem_cu13-3.4.5-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (60.4 MB)\n",
353
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m60.4/60.4 MB\u001b[0m \u001b[31m53.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
354
+ "\u001b[?25hDownloading triton-3.6.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (188.3 MB)\n",
355
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m188.3/188.3 MB\u001b[0m \u001b[31m34.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
356
+ "\u001b[?25hDownloading nvidia_cublas-13.1.0.3-py3-none-manylinux_2_27_x86_64.whl (423.1 MB)\n",
357
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m423.1/423.1 MB\u001b[0m \u001b[31m17.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
358
+ "\u001b[?25hDownloading nvidia_cuda_cupti-13.0.85-py3-none-manylinux_2_25_x86_64.whl (10.7 MB)\n",
359
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m10.7/10.7 MB\u001b[0m \u001b[31m56.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m0:01\u001b[0m\n",
360
+ "\u001b[?25hDownloading nvidia_cuda_nvrtc-13.0.88-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl (90.2 MB)\n",
361
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m90.2/90.2 MB\u001b[0m \u001b[31m52.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
362
+ "\u001b[?25hDownloading nvidia_cuda_runtime-13.0.96-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (2.2 MB)\n",
363
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m2.2/2.2 MB\u001b[0m \u001b[31m92.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
364
+ "\u001b[?25hDownloading nvidia_cufft-12.0.0.61-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (214.1 MB)\n",
365
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m214.1/214.1 MB\u001b[0m \u001b[31m24.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
366
+ "\u001b[?25hDownloading nvidia_cufile-1.15.1.6-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.2 MB)\n",
367
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m1.2/1.2 MB\u001b[0m \u001b[31m29.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m:00:01\u001b[0m\n",
368
+ "\u001b[?25hDownloading nvidia_curand-10.4.0.35-py3-none-manylinux_2_27_x86_64.whl (59.5 MB)\n",
369
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m59.5/59.5 MB\u001b[0m \u001b[31m56.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
370
+ "\u001b[?25hDownloading nvidia_cusolver-12.0.4.66-py3-none-manylinux_2_27_x86_64.whl (200.9 MB)\n",
371
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m200.9/200.9 MB\u001b[0m \u001b[31m34.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
372
+ "\u001b[?25hDownloading nvidia_cusparse-12.6.3.3-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (145.9 MB)\n",
373
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m145.9/145.9 MB\u001b[0m \u001b[31m35.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
374
+ "\u001b[?25hDownloading nvidia_nvjitlink-13.0.88-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl (40.7 MB)\n",
375
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m40.7/40.7 MB\u001b[0m \u001b[31m59.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
376
+ "\u001b[?25hDownloading nvidia_nvtx-13.0.85-py3-none-manylinux1_x86_64.manylinux_2_5_x86_64.whl (148 kB)\n",
377
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m148.0/148.0 kB\u001b[0m \u001b[31m24.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
378
+ "\u001b[?25hDownloading torchmetrics-1.9.0-py3-none-any.whl (983 kB)\n",
379
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m983.4/983.4 kB\u001b[0m \u001b[31m86.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
380
+ "\u001b[?25hDownloading ml_collections-1.1.0-py3-none-any.whl (76 kB)\n",
381
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m76.7/76.7 kB\u001b[0m \u001b[31m12.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
382
+ "\u001b[?25hDownloading mudata-0.3.3-py3-none-any.whl (43 kB)\n",
383
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m43.4/43.4 kB\u001b[0m \u001b[31m6.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
384
+ "\u001b[?25hDownloading pyro_ppl-1.9.1-py3-none-any.whl (755 kB)\n",
385
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m756.0/756.0 kB\u001b[0m \u001b[31m93.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
386
+ "\u001b[?25hDownloading rich-14.3.3-py3-none-any.whl (310 kB)\n",
387
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m310.5/310.5 kB\u001b[0m \u001b[31m44.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
388
+ "\u001b[?25hDownloading xarray-2026.2.0-py3-none-any.whl (1.4 MB)\n",
389
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m1.4/1.4 MB\u001b[0m \u001b[31m96.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
390
+ "\u001b[?25hDownloading cuda_bindings-13.2.0-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (6.3 MB)\n",
391
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m6.3/6.3 MB\u001b[0m \u001b[31m42.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m:00:01\u001b[0m\n",
392
+ "\u001b[?25hDownloading fsspec-2026.3.0-py3-none-any.whl (202 kB)\n",
393
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m202.6/202.6 kB\u001b[0m \u001b[31m3.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0mta \u001b[36m0:00:01\u001b[0m\n",
394
+ "\u001b[?25hDownloading lightning_utilities-0.15.3-py3-none-any.whl (31 kB)\n",
395
+ "Downloading markdown_it_py-4.0.0-py3-none-any.whl (87 kB)\n",
396
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m87.3/87.3 kB\u001b[0m \u001b[31m1.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0meta \u001b[36m0:00:01\u001b[0m\n",
397
+ "\u001b[?25hDownloading opt_einsum-3.4.0-py3-none-any.whl (71 kB)\n",
398
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m71.9/71.9 kB\u001b[0m \u001b[31m1.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m0:00:01\u001b[0m\n",
399
+ "\u001b[?25hDownloading pyro_api-0.1.2-py3-none-any.whl (11 kB)\n",
400
+ "Downloading scikit_misc-0.5.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (182 kB)\n",
401
+ "\u001b[2K \u001b[90m━━━━━━━━━━━���━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m183.0/183.0 kB\u001b[0m \u001b[31m5.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
402
+ "\u001b[?25hDownloading setuptools-81.0.0-py3-none-any.whl (1.1 MB)\n",
403
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m1.1/1.1 MB\u001b[0m \u001b[31m36.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
404
+ "\u001b[?25hDownloading sympy-1.14.0-py3-none-any.whl (6.3 MB)\n",
405
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m6.3/6.3 MB\u001b[0m \u001b[31m57.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m00:01\u001b[0m00:01\u001b[0m\n",
406
+ "\u001b[?25hDownloading filelock-3.25.2-py3-none-any.whl (26 kB)\n",
407
+ "Downloading pytorch_lightning-2.6.1-py3-none-any.whl (857 kB)\n",
408
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m857.3/857.3 kB\u001b[0m \u001b[31m8.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m:00:01\u001b[0m\n",
409
+ "\u001b[?25hDownloading aiohttp-3.13.5-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (1.8 MB)\n",
410
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m1.8/1.8 MB\u001b[0m \u001b[31m69.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
411
+ "\u001b[?25hDownloading cuda_pathfinder-1.5.2-py3-none-any.whl (49 kB)\n",
412
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m50.0/50.0 kB\u001b[0m \u001b[31m8.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
413
+ "\u001b[?25hDownloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)\n",
414
+ "Downloading mpmath-1.3.0-py3-none-any.whl (536 kB)\n",
415
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m536.2/536.2 kB\u001b[0m \u001b[31m62.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
416
+ "\u001b[?25hDownloading aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)\n",
417
+ "Downloading aiosignal-1.4.0-py3-none-any.whl (7.5 kB)\n",
418
+ "Downloading frozenlist-1.8.0-cp312-cp312-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (242 kB)\n",
419
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m242.4/242.4 kB\u001b[0m \u001b[31m35.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
420
+ "\u001b[?25hDownloading multidict-6.7.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (256 kB)\n",
421
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m256.3/256.3 kB\u001b[0m \u001b[31m58.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
422
+ "\u001b[?25hDownloading propcache-0.4.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (221 kB)\n",
423
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m221.6/221.6 kB\u001b[0m \u001b[31m30.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
424
+ "\u001b[?25hDownloading yarl-1.23.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (100 kB)\n",
425
+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m100.1/100.1 kB\u001b[0m \u001b[31m16.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
426
+ "\u001b[?25hBuilding wheels for collected packages: docrep\n",
427
+ " Building wheel for docrep (setup.py) ... \u001b[?25ldone\n",
428
+ "\u001b[?25h Created wheel for docrep: filename=docrep-0.3.2-py3-none-any.whl size=19971 sha256=258fce8926b494b98881dbea4108cc53884fb38800dfa648b7ac3a49087a8973\n",
429
+ " Stored in directory: /root/.cache/pip/wheels/d6/19/ee/0a6a1793d91c449563b49ccab57ce52da3e6fab7614836bd8c\n",
430
+ "Successfully built docrep\n",
431
+ "Installing collected packages: pyro-api, nvidia-cusparselt-cu13, mpmath, cuda-toolkit, triton, sympy, setuptools, scikit-misc, propcache, opt-einsum, nvidia-nvtx, nvidia-nvshmem-cu13, nvidia-nvjitlink, nvidia-nccl-cu13, nvidia-curand, nvidia-cufile, nvidia-cuda-runtime, nvidia-cuda-nvrtc, nvidia-cuda-cupti, nvidia-cublas, multidict, ml-collections, mdurl, lightning-utilities, fsspec, frozenlist, filelock, docrep, cuda-pathfinder, aiohappyeyeballs, yarl, sparse, nvidia-cusparse, nvidia-cufft, nvidia-cudnn-cu13, markdown-it-py, cuda-bindings, aiosignal, xarray, rich, nvidia-cusolver, aiohttp, mudata, torch, torchmetrics, pyro-ppl, pytorch-lightning, lightning, scvi-tools\n",
432
+ " Attempting uninstall: setuptools\n",
433
+ " Found existing installation: setuptools 82.0.1\n",
434
+ " Uninstalling setuptools-82.0.1:\n",
435
+ " Successfully uninstalled setuptools-82.0.1\n",
436
+ "Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.13.5 aiosignal-1.4.0 cuda-bindings-13.2.0 cuda-pathfinder-1.5.2 cuda-toolkit-13.0.2 docrep-0.3.2 filelock-3.25.2 frozenlist-1.8.0 fsspec-2026.3.0 lightning-2.6.1 lightning-utilities-0.15.3 markdown-it-py-4.0.0 mdurl-0.1.2 ml-collections-1.1.0 mpmath-1.3.0 mudata-0.3.3 multidict-6.7.1 nvidia-cublas-13.1.0.3 nvidia-cuda-cupti-13.0.85 nvidia-cuda-nvrtc-13.0.88 nvidia-cuda-runtime-13.0.96 nvidia-cudnn-cu13-9.19.0.56 nvidia-cufft-12.0.0.61 nvidia-cufile-1.15.1.6 nvidia-curand-10.4.0.35 nvidia-cusolver-12.0.4.66 nvidia-cusparse-12.6.3.3 nvidia-cusparselt-cu13-0.8.0 nvidia-nccl-cu13-2.28.9 nvidia-nvjitlink-13.0.88 nvidia-nvshmem-cu13-3.4.5 nvidia-nvtx-13.0.85 opt-einsum-3.4.0 propcache-0.4.1 pyro-api-0.1.2 pyro-ppl-1.9.1 pytorch-lightning-2.6.1 rich-14.3.3 scikit-misc-0.5.2 scvi-tools-1.4.2 setuptools-81.0.0 sparse-0.18.0 sympy-1.14.0 torch-2.11.0 torchmetrics-1.9.0 triton-3.6.0 xarray-2026.2.0 yarl-1.23.0\n",
437
+ "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n",
438
+ "\u001b[0mRequirement already satisfied: anndata in /usr/local/lib/python3.12/dist-packages (0.12.10)\n",
439
+ "Requirement already satisfied: array-api-compat>=1.7.1 in /usr/local/lib/python3.12/dist-packages (from anndata) (1.14.0)\n",
440
+ "Requirement already satisfied: h5py>=3.8 in /usr/local/lib/python3.12/dist-packages (from anndata) (3.16.0)\n",
441
+ "Requirement already satisfied: legacy-api-wrap in /usr/local/lib/python3.12/dist-packages (from anndata) (1.5)\n",
442
+ "Requirement already satisfied: natsort in /usr/local/lib/python3.12/dist-packages (from anndata) (8.4.0)\n",
443
+ "Requirement already satisfied: numpy>=1.26 in /usr/local/lib/python3.12/dist-packages (from anndata) (2.4.3)\n",
444
+ "Requirement already satisfied: packaging>=24.2 in /usr/local/lib/python3.12/dist-packages (from anndata) (26.0)\n",
445
+ "Requirement already satisfied: pandas!=2.1.2,<3,>=2.1.0 in /usr/local/lib/python3.12/dist-packages (from anndata) (2.3.3)\n",
446
+ "Requirement already satisfied: scipy!=1.17.0,>=1.12 in /usr/local/lib/python3.12/dist-packages (from anndata) (1.17.1)\n",
447
+ "Requirement already satisfied: zarr!=3.0.*,>=2.18.7 in /usr/local/lib/python3.12/dist-packages (from anndata) (3.1.6)\n",
448
+ "Requirement already satisfied: python-dateutil>=2.8.2 in /usr/local/lib/python3.12/dist-packages (from pandas!=2.1.2,<3,>=2.1.0->anndata) (2.9.0.post0)\n",
449
+ "Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.12/dist-packages (from pandas!=2.1.2,<3,>=2.1.0->anndata) (2026.1.post1)\n",
450
+ "Requirement already satisfied: tzdata>=2022.7 in /usr/local/lib/python3.12/dist-packages (from pandas!=2.1.2,<3,>=2.1.0->anndata) (2025.3)\n",
451
+ "Requirement already satisfied: donfig>=0.8 in /usr/local/lib/python3.12/dist-packages (from zarr!=3.0.*,>=2.18.7->anndata) (0.8.1.post1)\n",
452
+ "Requirement already satisfied: google-crc32c>=1.5 in /usr/local/lib/python3.12/dist-packages (from zarr!=3.0.*,>=2.18.7->anndata) (1.8.0)\n",
453
+ "Requirement already satisfied: numcodecs>=0.14 in /usr/local/lib/python3.12/dist-packages (from zarr!=3.0.*,>=2.18.7->anndata) (0.16.5)\n",
454
+ "Requirement already satisfied: typing-extensions>=4.12 in /usr/local/lib/python3.12/dist-packages (from zarr!=3.0.*,>=2.18.7->anndata) (4.15.0)\n",
455
+ "Requirement already satisfied: pyyaml in /usr/local/lib/python3.12/dist-packages (from donfig>=0.8->zarr!=3.0.*,>=2.18.7->anndata) (6.0.3)\n",
456
+ "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.12/dist-packages (from python-dateutil>=2.8.2->pandas!=2.1.2,<3,>=2.1.0->anndata) (1.17.0)\n",
457
+ "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n",
458
+ "\u001b[0mRequirement already satisfied: pandas in /usr/local/lib/python3.12/dist-packages (2.3.3)\n",
459
+ "Requirement already satisfied: numpy>=1.26.0 in /usr/local/lib/python3.12/dist-packages (from pandas) (2.4.3)\n",
460
+ "Requirement already satisfied: python-dateutil>=2.8.2 in /usr/local/lib/python3.12/dist-packages (from pandas) (2.9.0.post0)\n",
461
+ "Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.12/dist-packages (from pandas) (2026.1.post1)\n",
462
+ "Requirement already satisfied: tzdata>=2022.7 in /usr/local/lib/python3.12/dist-packages (from pandas) (2025.3)\n",
463
+ "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.12/dist-packages (from python-dateutil>=2.8.2->pandas) (1.17.0)\n",
464
+ "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n",
465
+ "\u001b[0mRequirement already satisfied: scipy in /usr/local/lib/python3.12/dist-packages (1.17.1)\n",
466
+ "Requirement already satisfied: numpy<2.7,>=1.26.4 in /usr/local/lib/python3.12/dist-packages (from scipy) (2.4.3)\n",
467
+ "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n",
468
+ "\u001b[0mRequirement already satisfied: scikit-learn in /usr/local/lib/python3.12/dist-packages (1.8.0)\n",
469
+ "Requirement already satisfied: numpy>=1.24.1 in /usr/local/lib/python3.12/dist-packages (from scikit-learn) (2.4.3)\n",
470
+ "Requirement already satisfied: scipy>=1.10.0 in /usr/local/lib/python3.12/dist-packages (from scikit-learn) (1.17.1)\n",
471
+ "Requirement already satisfied: joblib>=1.3.0 in /usr/local/lib/python3.12/dist-packages (from scikit-learn) (1.5.3)\n",
472
+ "Requirement already satisfied: threadpoolctl>=3.2.0 in /usr/local/lib/python3.12/dist-packages (from scikit-learn) (3.6.0)\n",
473
+ "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n",
474
+ "\u001b[0m"
475
+ ]
476
+ },
477
  {
478
  "name": "stderr",
479
  "output_type": "stream",
480
  "text": [
 
 
481
  "Seed set to 7\n"
482
  ]
483
  },
 
485
  "name": "stdout",
486
  "output_type": "stream",
487
  "text": [
488
+ "Kernel python: /usr/bin/python3\n",
489
+ "Project root: /root/final\n",
490
+ "Data root: /root/final/data/scPerturb\n",
491
+ "Metadata path: /root/final/data/processed/scPerturb/cell_metadata_standardized.csv\n",
492
+ "Output dir: /root/final/data/processed/scPerturb/latent_space\n",
493
+ "Figure dir: /root/final/data/processed/scPerturb/latent_space/figures\n",
494
  "scanpy version: 1.12\n",
495
  "scvi-tools version: 1.4.2\n",
496
+ "torch version: 2.11.0+cu130\n",
497
+ "torch.cuda.is_available: True\n",
498
+ "torch.backends.mps.is_available: False\n",
499
+ "SCVI accelerator/devices: gpu/1\n"
500
  ]
501
  }
502
  ],
503
  "source": [
504
+ "! pip install scanpy\n",
505
+ "! pip install scvi-tools\n",
506
+ "! pip install anndata\n",
507
+ "! pip install pandas\n",
508
+ "! pip install scipy\n",
509
+ "! pip install scikit-learn\n",
510
+ "! pip install torch\n",
511
+ "! pip install matplotlib\n",
512
  "from __future__ import annotations\n",
513
  "\n",
514
  "from pathlib import Path\n",
 
608
  },
609
  {
610
  "cell_type": "code",
611
+ "execution_count": 2,
612
  "id": "metadata-selection",
613
  "metadata": {},
614
  "outputs": [
 
691
  "0 0.002774 [CRISPR] "
692
  ]
693
  },
694
+ "execution_count": 2,
695
  "metadata": {},
696
  "output_type": "execute_result"
697
  }
 
744
  },
745
  {
746
  "cell_type": "code",
747
+ "execution_count": 3,
748
  "id": "helpers",
749
  "metadata": {},
750
  "outputs": [],
 
853
  },
854
  {
855
  "cell_type": "code",
856
+ "execution_count": 4,
857
  "id": "gene-space-build",
858
  "metadata": {},
859
  "outputs": [
 
950
  "ENSG00000187608 ENSG00000187608 2946.0 2180 ISG15"
951
  ]
952
  },
953
+ "execution_count": 4,
954
  "metadata": {},
955
  "output_type": "execute_result"
956
  }
 
1668
  },
1669
  {
1670
  "cell_type": "code",
1671
+ "execution_count": 5,
1672
  "id": "36db668b",
1673
  "metadata": {},
1674
  "outputs": [
 
1677
  "output_type": "stream",
1678
  "text": [
1679
  "[Step 1/11] Read dataset file\n",
1680
+ "Reading dataset: /root/final/data/scPerturb/rna_protein/ReplogleWeissman2022_K562_essential.h5ad\n",
1681
  "[FULL_RUN] Loaded full adata: n_obs=310385, n_vars=8563\n",
1682
  "[Step 2/11] Identify key metadata columns\n",
1683
  "obs columns count: 24\n",
 
1694
  "[FULL_RUN] Using all filtered cells: 310385\n",
1695
  "[Step 6/11] Normalize and log-transform expression\n",
1696
  "post-log1p matrix shape: (310385, 8563)\n",
1697
+ "[Step 7/11] Select HVGs\n",
1698
+ "HVG method: scanpy.seurat_v3 + layer=counts\n",
1699
+ "HVG selected: 3000\n",
1700
+ "[Step 8/11] Build target-gene and feature-gene masks\n",
1701
+ "target genes total: 2056\n",
1702
+ "target genes present in var: 1866\n",
1703
+ "feature genes total: 4334\n",
1704
+ "[Step 9/11] Build gene-level train/val/test split\n",
1705
+ "genes with split labels: 2056\n",
1706
+ "split counts:\n",
1707
+ "split\n",
1708
+ "train 248343\n",
1709
+ "test 33235\n",
1710
+ "val 28807\n",
1711
+ "Name: count, dtype: int64\n",
1712
+ "[Step 10/11] Restrict to feature genes\n",
1713
+ "genes filtered: 8563 -> 4334\n",
1714
+ "Saved prediction-ready h5ad: /root/final/data/processed/scPerturb/prediction_ready/replogle_k562_essential_single_gene_prediction_ready_full.h5ad\n",
1715
+ "Summary:\n",
1716
+ "dataset ReplogleWeissman2022_K562_essential\n",
1717
+ "n_cells 310385\n",
1718
+ "n_genes 4334\n",
1719
+ "n_controls 10816\n",
1720
+ "n_single_perturbed 299694\n",
1721
+ "split_counts {'train': 248343, 'test': 33235, 'val': 28807}\n",
1722
+ "hvg_method scanpy.seurat_v3 + layer=counts\n",
1723
+ "hvg_n_top_genes 3000\n",
1724
+ "n_target_genes_total 2056\n",
1725
+ "n_target_genes_present 1866\n",
1726
+ "n_feature_genes 4334\n",
1727
+ "dtype: object\n"
1728
  ]
1729
  }
1730
  ],
 
2009
  ],
2010
  "metadata": {
2011
  "kernelspec": {
2012
+ "display_name": "Python 3",
2013
  "language": "python",
2014
  "name": "python3"
2015
  },
 
2023
  "name": "python",
2024
  "nbconvert_exporter": "python",
2025
  "pygments_lexer": "ipython3",
2026
+ "version": "3.12.3"
2027
  }
2028
  },
2029
  "nbformat": 4,
src/data/replogle_k562_essential_scdfm_preprocess.ipynb CHANGED
The diff for this file is too large to render. See raw diff