Quality control
Summary
| Task | ✓ | ✗ | ✗✗ | ✗✗✗ |
|---|---|---|---|---|
| batch integration embed | 837 | |||
| batch integration feature | 546 | |||
| batch integration graph | 438 | |||
| cell cell communication ligand target | 109 | |||
| cell cell communication source target | 109 | |||
| denoising | 84 | 1 | 1 | |
| dimensionality reduction | 553 | 26 | 6 | 1 |
| label projection | 149 | |||
| matching modalities | 66 | |||
| task perturbation prediction | 161 | 2 | ||
| task spatial decomposition | 61 | 2 | 4 | 2 |
| task spatially variable genes | 105 | 17 | 1 | 1 |
Detailed
Tip
The tooltip contains some more details on the QC check.
| Task | Category | Name | Value | Condition | Severity |
|---|---|---|---|---|---|
| denoising | Scaling | Worst score knn_smoothing poisson | -10.2983151 | worst_score >= -1 | ✗✗✗ |
| task spatially variable genes | Raw results | Method ‘boostgp’ %missing | 0.7800000 | pct_missing <= .1 | ✗✗✗ |
| dimensionality reduction | Raw results | Dataset ‘zebrafish_labs’ %missing | 0.6000000 | pct_missing <= .1 | ✗✗✗ |
| task spatial decomposition | Scaling | Worst score cell2location r2 | -3.3126000 | worst_score >= -1 | ✗✗✗ |
| task spatial decomposition | Scaling | Worst score seurat r2 | -3.1724000 | worst_score >= -1 | ✗✗✗ |
| task perturbation prediction | Dataset info | Pct ‘task_id’ missing | 1.0000000 | percent_missing(dataset_info, field) | ✗✗ |
| task spatial decomposition | Dataset info | Pct ‘task_id’ missing | 1.0000000 | percent_missing(dataset_info, field) | ✗✗ |
| task perturbation prediction | Method info | Pct ‘paper_reference’ missing | 0.5000000 | percent_missing(method_info, field) | ✗✗ |
| task spatial decomposition | Method info | Pct ‘paper_reference’ missing | 0.8181818 | percent_missing(method_info, field) | ✗✗ |
| task spatial decomposition | Scaling | Worst score nnls r2 | -2.8586000 | worst_score >= -1 | ✗✗ |
| task spatial decomposition | Scaling | Worst score rctd r2 | -2.5379000 | worst_score >= -1 | ✗✗ |
| task spatially variable genes | Raw results | Dataset ‘zenodo_spatial/merfish/mouse_cortex’ %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 | ✗✗ |
| denoising | Scaling | Worst score alra_sqrt poisson | -2.3012026 | worst_score >= -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 spatial decomposition | Scaling | Worst score nmfreg r2 | -1.8296000 | worst_score >= -1 | ✗ |
| task spatially variable genes | Raw results | Method ‘spark’ %missing | 0.1600000 | pct_missing <= .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 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 spatially variable genes | Raw results | Method ‘somde’ %missing | 0.1200000 | pct_missing <= .1 | ✗ |
| task spatial decomposition | Scaling | Worst score destvi r2 | -1.1763000 | worst_score >= -1 | ✗ |