Quality control
Summary
| Task | ✓ | ✗ | ✗✗ | ✗✗✗ |
|---|---|---|---|---|
| cell cell communication ligand target | 109 | |||
| cell cell communication source target | 109 | |||
| denoising | 84 | 1 | 1 | |
| dimensionality reduction | 553 | 26 | 6 | 1 |
| matching modalities | 66 | |||
| spatial decomposition | 77 | 1 | 1 | |
| task batch integration | 701 | 19 | 11 | 15 |
| task label projection | 186 | 3 | 8 | 9 |
| task perturbation prediction | 160 | 3 | ||
| task predict modality | 182 | 5 | 6 | 1 |
| task spatially variable genes | 102 | 17 | 4 | 1 |
Detailed
Tip
The tooltip contains some more details on the QC check.
| Task | Category | Name | Value | Condition | Severity |
|---|---|---|---|---|---|
| task batch integration | Scaling | Best score bbknn ilisi | 35.0348000 | best_score <= 2 | ✗✗✗ |
| denoising | Scaling | Worst score knn_smoothing poisson | -10.2983151 | worst_score >= -1 | ✗✗✗ |
| task label projection | Raw results | Method ‘geneformer’ %missing | 1.0000000 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Method ‘scgpt_finetuned’ %missing | 1.0000000 | pct_missing <= .1 | ✗✗✗ |
| task label projection | Raw results | Method ‘scgpt_finetuned’ %missing | 1.0000000 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Method ‘scprint’ %missing | 1.0000000 | pct_missing <= .1 | ✗✗✗ |
| task label projection | Raw results | Method ‘scprint’ %missing | 1.0000000 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Method ‘batchelor_mnn_correct’ %missing | 0.8589744 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Method ‘mnnpy’ %missing | 0.8589744 | pct_missing <= .1 | ✗✗✗ |
| task spatially variable genes | Raw results | Method ‘boostgp’ %missing | 0.7800000 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Metric ‘hvg_overlap’ %missing | 0.7564103 | pct_missing <= .1 | ✗✗✗ |
| dimensionality reduction | Raw results | Dataset ‘zebrafish_labs’ %missing | 0.6000000 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Method ‘bbknn’ %missing | 0.5512821 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Scaling | Worst score seuratv3 r2 | -4.8476947 | worst_score >= -1 | ✗✗✗ |
| task batch integration | Raw results | Method ‘geneformer’ %missing | 0.4102564 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Method ‘scgpt_zeroshot’ %missing | 0.4102564 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Method ‘scimilarity’ %missing | 0.4102564 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Metric ‘kbet’ %missing | 0.4038462 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Dataset ‘cellxgene_census/hypomap’ %missing | 0.3786982 | pct_missing <= .1 | ✗✗✗ |
| task label projection | Raw results | Dataset ‘cellxgene_census/mouse_pancreas_atlas’ %missing | 0.3684211 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Metric ‘isolated_label_asw’ %missing | 0.3653846 | pct_missing <= .1 | ✗✗✗ |
| task predict modality | Raw results | Dataset ‘openproblems_neurips2022/pbmc_multiome/swap’ %missing | 0.3611111 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Dataset ‘cellxgene_census/mouse_pancreas_atlas’ %missing | 0.3579882 | pct_missing <= .1 | ✗✗✗ |
| task label projection | Raw results | Method ‘scgpt_zeroshot’ %missing | 0.3333333 | pct_missing <= .1 | ✗✗✗ |
| task label projection | Raw results | Method ‘scimilarity’ %missing | 0.3333333 | pct_missing <= .1 | ✗✗✗ |
| task label projection | Raw results | Method ‘scimilarity_knn’ %missing | 0.3333333 | pct_missing <= .1 | ✗✗✗ |
| task label projection | Raw results | Method ‘singler’ %missing | 0.3333333 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Raw results | Metric ‘isolated_label_f1’ %missing | 0.3333333 | pct_missing <= .1 | ✗✗✗ |
| task label projection | Raw results | Dataset ‘cellxgene_census/hypomap’ %missing | 0.3157895 | pct_missing <= .1 | ✗✗✗ |
| task batch integration | Dataset info | Pct ‘task_id’ missing | 1.0000000 | percent_missing(dataset_info, field) | ✗✗ |
| task label projection | Dataset info | Pct ‘task_id’ missing | 1.0000000 | percent_missing(dataset_info, field) | ✗✗ |
| task perturbation prediction | Dataset info | Pct ‘task_id’ missing | 1.0000000 | percent_missing(dataset_info, field) | ✗✗ |
| task predict modality | Dataset info | Pct ‘task_id’ missing | 1.0000000 | percent_missing(dataset_info, field) | ✗✗ |
| task spatially variable genes | Dataset info | Pct ‘task_id’ missing | 1.0000000 | percent_missing(dataset_info, field) | ✗✗ |
| task batch integration | Method info | Pct ‘paper_reference’ missing | 0.7307692 | percent_missing(method_info, field) | ✗✗ |
| task label projection | Method info | Pct ‘paper_reference’ missing | 0.8421053 | percent_missing(method_info, field) | ✗✗ |
| task perturbation prediction | Method info | Pct ‘paper_reference’ missing | 0.5000000 | percent_missing(method_info, field) | ✗✗ |
| task predict modality | Method info | Pct ‘paper_reference’ missing | 0.5555556 | percent_missing(method_info, field) | ✗✗ |
| task spatially variable genes | Method info | Pct ‘paper_reference’ missing | 0.8750000 | percent_missing(method_info, field) | ✗✗ |
| task batch integration | Metric info | Pct ‘paper_reference’ missing | 1.0000000 | percent_missing(metric_info, field) | ✗✗ |
| task label projection | Metric info | Pct ‘paper_reference’ missing | 1.0000000 | percent_missing(metric_info, field) | ✗✗ |
| task perturbation prediction | Metric info | Pct ‘paper_reference’ missing | 1.0000000 | percent_missing(metric_info, field) | ✗✗ |
| task predict modality | Metric info | Pct ‘paper_reference’ missing | 1.0000000 | percent_missing(metric_info, field) | ✗✗ |
| task spatially variable genes | Metric info | Pct ‘paper_reference’ missing | 1.0000000 | percent_missing(metric_info, field) | ✗✗ |
| task batch integration | Raw results | Dataset ‘cellxgene_census/dkd’ %missing | 0.2810651 | pct_missing <= .1 | ✗✗ |
| spatial decomposition | Scaling | Worst score tangram r2 | -2.6383322 | worst_score >= -1 | ✗✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/merfish/mouse_cortex’ %missing | 0.2500000 | pct_missing <= .1 | ✗✗ |
| task predict modality | Raw results | Method ‘guanlab_dengkw_pm’ %missing | 0.2500000 | pct_missing <= .1 | ✗✗ |
| task predict modality | Raw results | Method ‘zeros’ %missing | 0.2500000 | pct_missing <= .1 | ✗✗ |
| dimensionality reduction | Raw results | Metric ‘continuity’ %missing | 0.2500000 | pct_missing <= .1 | ✗✗ |
| dimensionality reduction | Raw results | Metric ‘lcmc’ %missing | 0.2500000 | pct_missing <= .1 | ✗✗ |
| dimensionality reduction | Raw results | Metric ‘qglobal’ %missing | 0.2500000 | pct_missing <= .1 | ✗✗ |
| dimensionality reduction | Raw results | Metric ‘qlocal’ %missing | 0.2500000 | pct_missing <= .1 | ✗✗ |
| dimensionality reduction | Raw results | Metric ‘qnn’ %missing | 0.2500000 | pct_missing <= .1 | ✗✗ |
| dimensionality reduction | Raw results | Metric ‘qnn_auc’ %missing | 0.2500000 | pct_missing <= .1 | ✗✗ |
| task predict modality | Scaling | Worst score lmds_irlba_rf overall_pearson | -2.4102000 | worst_score >= -1 | ✗✗ |
| denoising | Scaling | Worst score alra_sqrt poisson | -2.3012026 | worst_score >= -1 | ✗✗ |
| task label projection | Raw results | Metric ‘accuracy’ %missing | 0.2280702 | pct_missing <= .1 | ✗✗ |
| task label projection | Raw results | Metric ‘f1_macro’ %missing | 0.2280702 | pct_missing <= .1 | ✗✗ |
| task label projection | Raw results | Metric ‘f1_micro’ %missing | 0.2280702 | pct_missing <= .1 | ✗✗ |
| task label projection | Raw results | Metric ‘f1_weighted’ %missing | 0.2280702 | pct_missing <= .1 | ✗✗ |
| task batch integration | Raw results | Metric ‘asw_label’ %missing | 0.2243590 | pct_missing <= .1 | ✗✗ |
| task batch integration | Raw results | Dataset ‘cellxgene_census/tabula_sapiens’ %missing | 0.2218935 | pct_missing <= .1 | ✗✗ |
| task batch integration | Raw results | Dataset ‘cellxgene_census/gtex_v9’ %missing | 0.2189349 | pct_missing <= .1 | ✗✗ |
| task batch integration | Raw results | Dataset ‘cellxgene_census/immune_cell_atlas’ %missing | 0.2189349 | pct_missing <= .1 | ✗✗ |
| task batch integration | Raw results | Metric ‘asw_batch’ %missing | 0.2179487 | pct_missing <= .1 | ✗✗ |
| task batch integration | Raw results | Metric ‘cell_cycle_conservation’ %missing | 0.2179487 | pct_missing <= .1 | ✗✗ |
| task batch integration | Raw results | Metric ‘pcr’ %missing | 0.2179487 | pct_missing <= .1 | ✗✗ |
| task label projection | Raw results | Dataset ‘cellxgene_census/immune_cell_atlas’ %missing | 0.2105263 | pct_missing <= .1 | ✗✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/seqfish/mouse_organogenesis_seqfish’ %missing | 0.1875000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/slideseqv2/mouse_cortex’ %missing | 0.1875000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/stereoseq/drosophila_embryo_e6_3’ %missing | 0.1875000 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Metric ‘ari’ %missing | 0.1794872 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Metric ‘clisi’ %missing | 0.1794872 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Metric ‘graph_connectivity’ %missing | 0.1794872 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Metric ‘ilisi’ %missing | 0.1794872 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Metric ‘nmi’ %missing | 0.1794872 | pct_missing <= .1 | ✗ |
| task predict modality | Raw results | Metric ‘overall_pearson’ %missing | 0.1666667 | pct_missing <= .1 | ✗ |
| task predict modality | Raw results | Metric ‘overall_spearman’ %missing | 0.1666667 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Method ‘spark’ %missing | 0.1600000 | pct_missing <= .1 | ✗ |
| task label projection | Raw results | Dataset ‘cellxgene_census/dkd’ %missing | 0.1578947 | pct_missing <= .1 | ✗ |
| task label projection | Raw results | Dataset ‘cellxgene_census/gtex_v9’ %missing | 0.1578947 | pct_missing <= .1 | ✗ |
| task label projection | Raw results | Dataset ‘cellxgene_census/tabula_sapiens’ %missing | 0.1578947 | pct_missing <= .1 | ✗ |
| task batch integration | Scaling | Worst score scanorama hvg_overlap | -1.5279000 | worst_score >= -1 | ✗ |
| dimensionality reduction | Raw results | Method ‘densmap_logCP10k’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘densmap_logCP10k_1kHVG’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘densmap_pca_logCP10k’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘densmap_pca_logCP10k_1kHVG’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘diffusion_map’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘neuralee_default’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘neuralee_logCP10k_1kHVG’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘pca_logCP10k’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘pca_logCP10k_1kHVG’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘phate_default’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘phate_logCP10k’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘phate_logCP10k_1kHVG’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘phate_sqrt’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘pymde_distances_log_cp10k’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘pymde_distances_log_cp10k_hvg’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘pymde_neighbors_log_cp10k’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘pymde_neighbors_log_cp10k_hvg’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘random_features’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘spectral_features’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘true_features’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘tsne_logCP10k’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘tsne_logCP10k_1kHVG’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘umap_logCP10k’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘umap_logCP10k_1kHVG’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘umap_pca_logCP10k’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| dimensionality reduction | Raw results | Method ‘umap_pca_logCP10k_1kHVG’ %missing | 0.1500000 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘uce’ %missing | 0.1410256 | pct_missing <= .1 | ✗ |
| task predict modality | Raw results | Dataset ‘openproblems_neurips2022/pbmc_multiome/normal’ %missing | 0.1388889 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘batchelor_fastmnn’ %missing | 0.1282051 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘harmony’ %missing | 0.1282051 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘harmonypy’ %missing | 0.1282051 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘liger’ %missing | 0.1282051 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘pyliger’ %missing | 0.1282051 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘scanvi’ %missing | 0.1282051 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘scvi’ %missing | 0.1282051 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘tenx_visium/visium/human_brain_cancer’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘tenx_visium/visium/human_normal_prostate’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/slideseqv2/mouse_cerebellum’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/slideseqv2/mouse_hippocampus_puck’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/slideseqv2/mouse_olfactory_bulb_puck’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/slideseqv2/mouse_somatosensory_cortex_puck’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/starmap/mouse_brain_2d_zstep10_0’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/starmap/mouse_brain_2d_zstep15_0’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/stereoseq/drosophila_embryo_e10’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/stereoseq/drosophila_embryo_e5_6’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/stereoseq/drosophila_embryo_e7’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/stereoseq/drosophila_embryo_e9_1’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task predict modality | Raw results | Method ‘knnr_py’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task predict modality | Raw results | Method ‘lm’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| task batch integration | Scaling | Worst score scalex hvg_overlap | -1.2449000 | worst_score >= -1 | ✗ |
| task spatially variable genes | Raw results | Method ‘somde’ %missing | 0.1200000 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘embed_cell_types’ %missing | 0.1153846 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘embed_cell_types_jittered’ %missing | 0.1153846 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘no_integration’ %missing | 0.1153846 | pct_missing <= .1 | ✗ |
| task batch integration | Raw results | Method ‘no_integration_batch’ %missing | 0.1153846 | pct_missing <= .1 | ✗ |