scDrugPerturb-Bench / release_audit.json
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{
"schema_version": 1,
"status": "PASS",
"summary": {
"datasets": 20,
"files": 60,
"bytes": 32661867329,
"checks": 764,
"failures": 0,
"warnings": 11
},
"global_checks": [
{
"name": "selection_count",
"passed": true,
"detail": "found 20 rows"
},
{
"name": "benchmark_ids_unique",
"passed": true,
"detail": "benchmark IDs must be unique"
},
{
"name": "pmids_unique",
"passed": true,
"detail": "found 20 unique PMIDs"
},
{
"name": "ranks_complete",
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"detail": "ranks must be 1 through 20"
}
],
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"warnings": [
"38937474_01: JSON groups absent from string/categorical obs values: 38937474_01_01:time_groups=20 days; 38937474_01_02:time_groups=20 days; 38937474_01_03:time_groups=20 days; 38937474_01_04:time_groups=20 days; 38937474_01_05:time_groups=20 days",
"40766395_01: JSON groups absent from string/categorical obs values: 40766395_01_01:time_groups=24 h",
"37086265_01: test cases with no target genes (not evaluable): 37086265_01_03",
"37086265_01: JSON groups absent from string/categorical obs values: 37086265_01_01:dose_groups=50 uM; 37086265_01_02:dose_groups=50 uM; 37086265_01_03:dose_groups=50 uM; 37086265_01_04:dose_groups=50 uM; 37086265_01_05:dose_groups=50 uM; 37086265_01_06:dose_groups=50 uM",
"36318267_01: JSON groups absent from string/categorical obs values: 36318267_01_01:time_groups=2 day",
"41871169_01: test cases with no target genes (not evaluable): 41871169_01_05",
"41871169_01: JSON groups absent from string/categorical obs values: 41871169_01_03:time_groups=2 day; 41871169_01_04:time_groups=2 day; 41871169_01_05:time_groups=2 day",
"32094658_01: control/treated var gene order differs; downstream joins must align by var_names",
"39803533_01: JSON groups absent from string/categorical obs values: 39803533_01_01:time_groups=2.5 hours; 39803533_01_03:time_groups=2.5 hours",
"40166195_01: JSON groups absent from string/categorical obs values: 40166195_01_01:dose_groups=400 nM",
"34857732_01: 6 obs_names occur in both control and ground_truth; use sample_id/split when concatenating"
],
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{
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{
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{
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{
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"detail": "DOWN,UP"
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{
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{
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{
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{
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{
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{
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{
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},
"target_genes": [
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"AGER",
"AQP4",
"BPIFB1",
"BPIFB2",
"CDH2",
"CENPF",
"CLIC5",
"CNN1",
"CYP4B1",
"DIAPH2",
"LMNA",
"LMNB1",
"LMNB2",
"MATN2",
"MUC5B",
"MYH14",
"MYH9",
"MYL9",
"MYLK",
"PIGR",
"RHOB",
"RHOBTB3",
"RND3",
"SCGB3A1",
"SERPINE1",
"SFTPD",
"SNAI2",
"SPDL1",
"SPOCK1",
"TAGLN",
"TNNC1",
"TRIO",
"TWIST1"
]
},
{
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{
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{
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{
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},
{
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"passed": true,
"detail": "UP"
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{
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{
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"detail": "JSON=18, selection=18"
},
{
"name": "control_nonempty",
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{
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{
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"detail": "var_names"
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"pct_counts_hb",
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"scrublet_doublet_score",
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"fail_hard",
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"pct_mt",
"pct_counts_ribo",
"pct_counts_hb",
"log10_genes_per_umi",
"sparsity",
"scrublet_doublet_score",
"scrublet_predicted_doublet",
"soup_score",
"pct_top20",
"total_counts_mt",
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},
"target_genes": [
"ATF3",
"B2M",
"CD47",
"CD55",
"CD59",
"CD63",
"CXCL1",
"CXCL8",
"DDIT3",
"HLA-B",
"HLA-C",
"IRF7",
"IRF9",
"JUN",
"JUNB",
"MAFF",
"PLSCR1",
"SP100"
]
},
{
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"pmid": "34591417",
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},
{
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}
]
}