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 | |||
| perturbation prediction | 161 | 2 | ||
| spatial decomposition | 72 | 3 | 1 | 16 |
| spatially variable genes | 107 | 15 | 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 | ✗✗✗ |
| spatially variable genes | Raw results | Method ‘boostgp’ %missing | 0.8000000 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw results | Method ‘destvi’ %missing | 0.7575758 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw results | Method ‘rctd’ %missing | 0.6969697 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw results | Metric ‘r2’ %missing | 0.6776860 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw data | Number of results | 121.0000000 | len(results) == len(method_info) * len(metric_info) * len(dataset_info) | ✗✗✗ |
| spatial decomposition | Raw results | Method ‘cell2location’ %missing | 0.6666667 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw results | Method ‘nmfreg’ %missing | 0.6666667 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw results | Method ‘nnls’ %missing | 0.6666667 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw results | Method ‘random_proportions’ %missing | 0.6666667 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw results | Method ‘seurat’ %missing | 0.6666667 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw results | Method ‘stereoscope’ %missing | 0.6666667 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw results | Method ‘tangram’ %missing | 0.6666667 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw results | Method ‘true_proportions’ %missing | 0.6666667 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Raw results | Method ‘vanillanmf’ %missing | 0.6666667 | pct_missing <= .1 | ✗✗✗ |
| dimensionality reduction | Raw results | Dataset ‘zebrafish_labs’ %missing | 0.6000000 | pct_missing <= .1 | ✗✗✗ |
| spatial decomposition | Scaling | Worst score cell2location r2 | -3.4575000 | worst_score >= -1 | ✗✗✗ |
| spatial decomposition | Scaling | Worst score nnls r2 | -3.3901000 | worst_score >= -1 | ✗✗✗ |
| spatial decomposition | Scaling | Worst score seurat r2 | -3.0585000 | worst_score >= -1 | ✗✗✗ |
| perturbation prediction | Method info | Pct ‘paper_reference’ missing | 0.4166667 | percent_missing(method_info, field) | ✗✗ |
| perturbation prediction | Metric info | Pct ‘paper_reference’ missing | 1.0000000 | percent_missing(metric_info, field) | ✗✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/mouse_cortex_merfish’ %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 | ✗✗ |
| spatial decomposition | Scaling | Worst score nmfreg r2 | -2.2265000 | worst_score >= -1 | ✗✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/drosophila_embryo_e5_6’ %missing | 0.1875000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/mouse_cortex_slideseqv2’ %missing | 0.1875000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/mouse_organogenesis_seqfish’ %missing | 0.1875000 | pct_missing <= .1 | ✗ |
| spatial decomposition | Raw results | Dataset ‘cellxgene_census/tabula_sapiens’ %missing | 0.1818182 | pct_missing <= .1 | ✗ |
| spatial decomposition | Raw results | Dataset ‘cellxgene_census/tabula_sapiens’ %missing | 0.1818182 | pct_missing <= .1 | ✗ |
| spatial decomposition | Raw results | Dataset ‘cellxgene_census/tabula_sapiens’ %missing | 0.1818182 | 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 | ✗ |
| spatially variable genes | Raw results | Method ‘spark’ %missing | 0.1400000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘10x_datasets/human_breast_cancer_1_visium’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/drosophila_embryo_e10_stereoseq’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/drosophila_embryo_e6_3_stereoseq’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/drosophila_embryo_e7_stereoseq’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/drosophila_embryo_e9_1_stereoseq’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/mouse_cerebellum_slideseqv2’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/mouse_hippocampus_puck_slideseqv2’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/mouse_olfactory_bulb_puck_slideseqv2’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial/mouse_somatosensory_cortex_puck_slideseqv2’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Dataset ‘zenodo_spatial_slidetags/human_skin_melanoma_slidetags’ %missing | 0.1250000 | pct_missing <= .1 | ✗ |
| spatially variable genes | Raw results | Method ‘somde’ %missing | 0.1200000 | pct_missing <= .1 | ✗ |