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 77 1 1
spatially variable genes 107 15 1 1

Detailed

Tip

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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 ✗✗✗
dimensionality reduction Raw results Dataset ‘zebrafish_labs’ %missing 0.6000000 pct_missing <= .1 ✗✗✗
spatial decomposition Scaling Worst score seuratv3 r2 -4.8476947 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) ✗✗
spatial decomposition Scaling Worst score tangram r2 -2.6383322 worst_score >= -1 ✗✗
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 ✗✗
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
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