Major update of checkatlas after 2 years

data/modules/checkatlas/adata/B-cells_compartment.tsv

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+atlas_obs	obsm	var	varm	uns
+<code>donor_id</code><br><code>Predicted_labels_CellTypist</code><br><code>Majority_voting_CellTypist</code><br><code>Manually_curated_celltype</code><br><code>assay_ontology_term_id</code><br><code>cell_type_ontology_term_id</code><br><code>development_stage_ontology_term_id</code><br><code>disease_ontology_term_id</code><br><code>self_reported_ethnicity_ontology_term_id</code><br><code>is_primary_data</code><br><code>organism_ontology_term_id</code><br><code>sex_ontology_term_id</code><br><code>tissue_ontology_term_id</code><br><code>suspension_type</code><br><code>tissue_type</code><br><code>cell_type</code><br><code>assay</code><br><code>disease</code><br><code>organism</code><br><code>sex</code><br><code>tissue</code><br><code>self_reported_ethnicity</code><br><code>development_stage</code><br><code>observation_joinid</code>	<code>X_umap</code>	<code>gene_symbols</code><br><code>feature_is_filtered</code><br><code>feature_name</code><br><code>feature_reference</code><br><code>feature_biotype</code><br><code>feature_length</code><br><code>feature_type</code>	<code></code>	<code>cell_type_ontology_term_id_colors</code><br><code>citation</code><br><code>default_embedding</code><br><code>schema_reference</code><br><code>schema_version</code><br><code>sex_ontology_term_id_colors</code><br><code>title</code>

data/modules/checkatlas/adata/Fetal.tsv

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+atlas_obs	obsm	var	varm	uns
+<code>orig.ident</code><br><code>nCount_RNA</code><br><code>nFeature_RNA</code><br><code>seurat_clusters</code><br><code>donor_id</code><br><code>Stage</code><br><code>Selection</code><br><code>compartment</code><br><code>age</code><br><code>CnT</code><br><code>DTLH</code><br><code>UBCD</code><br><code>SSBpr</code><br><code>End</code><br><code>MSC</code><br><code>RVCSB</code><br><code>SSBpod</code><br><code>SSBm.d</code><br><code>ICa</code><br><code>ErPrT</code><br><code>ICb</code><br><code>NPC</code><br><code>Pod</code><br><code>annotCell</code><br><code>author_cell_type</code><br><code>cell_type_ontology_term_id</code><br><code>disease_ontology_term_id</code><br><code>self_reported_ethnicity_ontology_term_id</code><br><code>development_stage_ontology_term_id</code><br><code>tissue_ontology_term_id</code><br><code>sex_ontology_term_id</code><br><code>organism_ontology_term_id</code><br><code>is_primary_data</code><br><code>assay_ontology_term_id</code><br><code>suspension_type</code><br><code>tissue_type</code><br><code>cell_type</code><br><code>assay</code><br><code>disease</code><br><code>organism</code><br><code>sex</code><br><code>tissue</code><br><code>self_reported_ethnicity</code><br><code>development_stage</code><br><code>observation_joinid</code>	<code>X_pca</code><br><code>X_umap</code>	<code>vst.mean</code><br><code>vst.variance</code><br><code>vst.variance.expected</code><br><code>vst.variance.standardized</code><br><code>vst.variable</code><br><code>feature_is_filtered</code><br><code>feature_name</code><br><code>feature_reference</code><br><code>feature_biotype</code><br><code>feature_length</code><br><code>feature_type</code>	<code></code>	<code>citation</code><br><code>schema_reference</code><br><code>schema_version</code><br><code>title</code>

data/modules/checkatlas/adata/Tabula_Sapiens_Endothelial.tsv

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+atlas_obs	obsm	var	varm	uns
+<code>donor_id</code><br><code>tissue_in_publication</code><br><code>anatomical_position</code><br><code>method</code><br><code>cdna_plate</code><br><code>library_plate</code><br><code>notes</code><br><code>cdna_well</code><br><code>assay_ontology_term_id</code><br><code>sample_id</code><br><code>replicate</code><br><code>10X_run</code><br><code>ambient_removal</code><br><code>donor_method</code><br><code>donor_assay</code><br><code>donor_tissue</code><br><code>donor_tissue_assay</code><br><code>cell_type_ontology_term_id</code><br><code>compartment</code><br><code>broad_cell_class</code><br><code>free_annotation</code><br><code>manually_annotated</code><br><code>published_2022</code><br><code>n_genes_by_counts</code><br><code>total_counts</code><br><code>total_counts_mt</code><br><code>pct_counts_mt</code><br><code>total_counts_ercc</code><br><code>pct_counts_ercc</code><br><code>_scvi_batch</code><br><code>_scvi_labels</code><br><code>scvi_leiden_donorassay_full</code><br><code>ethnicity_original</code><br><code>scvi_leiden_res05_compartment</code><br><code>sample_number</code><br><code>organism_ontology_term_id</code><br><code>suspension_type</code><br><code>tissue_type</code><br><code>disease_ontology_term_id</code><br><code>is_primary_data</code><br><code>tissue_ontology_term_id</code><br><code>sex_ontology_term_id</code><br><code>self_reported_ethnicity_ontology_term_id</code><br><code>development_stage_ontology_term_id</code><br><code>cell_type</code><br><code>assay</code><br><code>disease</code><br><code>organism</code><br><code>sex</code><br><code>tissue</code><br><code>self_reported_ethnicity</code><br><code>development_stage</code><br><code>observation_joinid</code>	<code>X_compartment_uncorrected_umap</code><br><code>X_pca</code><br><code>X_scvi</code><br><code>X_umap</code><br><code>X_umap_compartment_scvi_donorassay</code><br><code>X_umap_scvi_full_donorassay</code><br><code>X_uncorrected_umap</code>	<code>ensembl_id</code><br><code>genome</code><br><code>mt</code><br><code>ercc</code><br><code>n_cells_by_counts</code><br><code>mean_counts</code><br><code>pct_dropout_by_counts</code><br><code>total_counts</code><br><code>mean</code><br><code>std</code><br><code>feature_is_filtered</code><br><code>feature_name</code><br><code>feature_reference</code><br><code>feature_biotype</code><br><code>feature_length</code><br><code>feature_type</code>	<code>PCs</code>	<code>_scvi_manager_uuid</code><br><code>_scvi_uuid</code><br><code>_training_mode</code><br><code>assay_ontology_term_id_colors</code><br><code>citation</code><br><code>compartment_colors</code><br><code>donor_id_colors</code><br><code>leiden</code><br><code>method_colors</code><br><code>neighbors</code><br><code>pca</code><br><code>schema_reference</code><br><code>schema_version</code><br><code>sex_ontology_term_id_colors</code><br><code>tissue_in_publication_colors</code><br><code>title</code><br><code>umap</code>

data/modules/checkatlas/annotation/B-cells_compartment.tsv

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+Annot_Sample	Reference	obs	rand_index	rand_index_running_time
+B-cells_compartment_cell_type	Manually_curated_celltype	cell_type	0.9767814794030185	0.021879196166992188
+B-cells_compartment_cell_type_ontology_term_id	Manually_curated_celltype	cell_type_ontology_term_id	0.9767814794030185	0.019063472747802734

data/modules/checkatlas/annotation/Fetal.tsv

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+Annot_Sample	Reference	obs	rand_index	rand_index_running_time
+Fetal_cell_type	author_cell_type	cell_type	0.9338405682824856	0.015674591064453125
+Fetal_cell_type_ontology_term_id	author_cell_type	cell_type_ontology_term_id	0.9338405682824856	0.011783123016357422
+Fetal_orig.ident	author_cell_type	orig.ident	0.8458873605141566	0.010969161987304688
+Fetal_seurat_clusters	author_cell_type	seurat_clusters	0.9301595090946928	0.011272668838500977

data/modules/checkatlas/annotation/Tabula_Sapiens_Endothelial.tsv

@@ -0,0 +1,4 @@
+Annot_Sample	Reference	obs	rand_index	rand_index_running_time
+Tabula_Sapiens_Endothelial_cell_type_ontology_term_id	cell_type	cell_type_ontology_term_id	1.0	0.03469395637512207
+Tabula_Sapiens_Endothelial_scvi_leiden_donorassay_full	cell_type	scvi_leiden_donorassay_full	0.4981544691977149	0.029968738555908203
+Tabula_Sapiens_Endothelial_scvi_leiden_res05_compartment	cell_type	scvi_leiden_res05_compartment	0.7180329859467465	0.03561878204345703