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| "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", |
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| "MYH14", |
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| "MYL9", |
| "MYLK", |
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| "RHOB", |
| "RHOBTB3", |
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| "SCGB3A1", |
| "SERPINE1", |
| "SFTPD", |
| "SNAI2", |
| "SPDL1", |
| "SPOCK1", |
| "TAGLN", |
| "TNNC1", |
| "TRIO", |
| "TWIST1" |
| ] |
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