├── .github └── workflows │ ├── clustering-ci.yml │ ├── filtering-ci.yml │ ├── ingestion-ci.yml │ ├── integration-ci.yml │ ├── integration01-ci.yml │ ├── integration02-ci.yml │ ├── integration03-ci.yml │ ├── refmap-ci.yml │ ├── spatial_deconvolution_cell2location-ci.yml │ ├── spatial_deconvolution_tangram-ci.yml │ ├── spatial_ingestion_merfish-ci.yml │ ├── spatial_ingestion_merscope-ci.yml │ ├── spatial_ingestion_visium-ci.yml │ ├── spatial_ingestion_xenium.yml │ ├── spatial_preprocess-ci.yml │ ├── spatial_preprocess_concat-ci.yml │ └── visualization-ci.yml ├── .gitignore ├── .readthedocs.yaml ├── CHANGELOG.md ├── CITATION.cff ├── LICENSE ├── README.md ├── docs ├── common_errors_rescomp.md ├── conf.py ├── contribute_guidelines.md ├── contributors.md ├── generated │ └── panpipes.rst ├── github_ssh_keys.md ├── img │ ├── Panpipes_Figure1_v21024_1.png │ ├── anndata_schema.svg │ ├── background_plot1.png │ ├── clr_margins.png │ ├── figure1_simplified.drawio.png │ ├── integration_coloured.drawio.png │ ├── mudata_paper.svg │ ├── panpipes_cropped_gif.gif │ ├── panpipes_logo.png │ ├── panpipes_logo3.png │ ├── panpipes_logo_small.png │ └── panpipeslogo2.png ├── index.rst ├── install.md ├── installation_rescomp.md ├── references.rst ├── release_notes.md ├── requirements.txt ├── tutorials │ ├── Guide_to_annotation.ipynb │ ├── Guide_to_annotation.md │ └── index.md ├── usage │ ├── different_entry_points.md │ ├── filter_dict_instructions.md │ ├── gene_list_format.md │ ├── general_principles.md │ ├── index.md │ ├── integration_methods.md │ ├── normalization_methods.md │ ├── panpipes_scverse.md │ ├── sample_file_qc_mm.md │ ├── sample_file_qc_mm.txt │ ├── setup_for_qc_mm.md │ ├── setup_for_spatial_workflows.md │ └── troubleshooting.md ├── workflows │ ├── clustering.md │ ├── clustering_spatial.md │ ├── deconvolute_spatial.md │ ├── index.rst │ ├── ingest_spatial.md │ ├── integration.md │ ├── pipeline_preprocess_preprint.yml │ ├── preprocess.md │ ├── preprocess_spatial.md │ ├── qc.md │ ├── refmap.md │ └── vis.md └── yaml_docs │ ├── index.rst │ ├── pipeline_clustering_yml.md │ ├── pipeline_ingestion_yml.md │ ├── pipeline_integration_yml.md │ ├── pipeline_preprocess_yml.md │ ├── pipeline_refmap_yml.md │ ├── pipeline_visualization_yml.md │ ├── spatial_deconvolution.md │ ├── spatial_preprocess.md │ ├── spatial_qc.md │ ├── threads_tasks_panpipes.md │ └── useful_info_on_yml.md ├── panpipes ├── .DS_Store ├── R_scripts │ ├── __init__.py │ ├── install_R_libs.R │ ├── plotQC.R │ ├── plot_cluster_metrics.R │ ├── plot_metrics.R │ ├── plotclustree.R │ ├── produce_barplot_10xmetric.v3.R │ └── refmap_wnn.R ├── __init__.py ├── entry.py ├── funcs.py ├── funcs │ ├── __init__.py │ ├── io.py │ ├── plotting.py │ ├── processing.py │ └── scmethods.py ├── panpipes │ ├── __init__.py │ ├── pipeline_clustering.py │ ├── pipeline_clustering │ │ └── pipeline.yml │ ├── pipeline_deconvolution_spatial.py │ ├── pipeline_deconvolution_spatial │ │ └── pipeline.yml │ ├── pipeline_ingest.py │ ├── pipeline_ingest │ │ └── pipeline.yml │ ├── pipeline_integration.py │ ├── pipeline_integration │ │ └── pipeline.yml │ ├── pipeline_preprocess.py │ ├── pipeline_preprocess │ │ └── pipeline.yml │ ├── pipeline_preprocess_spatial.py │ ├── pipeline_preprocess_spatial │ │ └── pipeline.yml │ ├── pipeline_qc_spatial.py │ ├── pipeline_qc_spatial │ │ └── pipeline.yml │ ├── pipeline_refmap.py │ ├── pipeline_refmap │ │ └── pipeline.yml │ ├── pipeline_vis.py │ └── pipeline_vis │ │ └── pipeline.yml ├── python_scripts │ ├── __init__.py │ ├── aggregate_cellranger_summary_metrics.py │ ├── aggregate_csvs.py │ ├── assess_background.py │ ├── batch_correct_bbknn.py │ ├── batch_correct_combat.py │ ├── batch_correct_harmony.py │ ├── batch_correct_merge.py │ ├── batch_correct_mofa.py │ ├── batch_correct_multivi.py │ ├── batch_correct_none.py │ ├── batch_correct_scanorama.py │ ├── batch_correct_scvi.py │ ├── batch_correct_totalvi.py │ ├── batch_correct_wnn.py │ ├── collate_mdata.py │ ├── concat_adata.py │ ├── concatenation_spatial.py │ ├── downsample.py │ ├── generate_cellxgene.py │ ├── integrate_wnn.py │ ├── make_adata_from_csv.py │ ├── make_spatialData_from_csv.py │ ├── plot_atac_qc.py │ ├── plot_cluster_umaps.py │ ├── plot_custom_markers.py │ ├── plot_custom_markers_umap.py │ ├── plot_features_scatter.py │ ├── plot_pca.py │ ├── plot_qc_spatial.py │ ├── plot_scanpy_markers.py │ ├── plot_umaps_batch_correct.py │ ├── plot_variables_umaps.py │ ├── refmap_generatescanvi.py │ ├── refmap_plot_umaps.py │ ├── refmap_scib.py │ ├── refmap_scvitools.py │ ├── rerun_find_neighbors_for_clustering.py │ ├── run_cell2location.py │ ├── run_clustering.py │ ├── run_collate_mtd_files.py │ ├── run_differential_peaks_ATAC.py │ ├── run_dsb_clr.py │ ├── run_filter.py │ ├── run_filter_spatial.py │ ├── run_find_markers.py │ ├── run_find_markers_multi.py │ ├── run_find_neighbors.py │ ├── run_lisi.py │ ├── run_preprocess_atac.py │ ├── run_preprocess_prot.py │ ├── run_preprocess_rna.py │ ├── run_preprocess_spatial.py │ ├── run_scanpyQC_atac.py │ ├── run_scanpyQC_prot.py │ ├── run_scanpyQC_rep.py │ ├── run_scanpyQC_rna.py │ ├── run_scanpyQC_spatial.py │ ├── run_scib.py │ ├── run_scib_metrics.py │ ├── run_scrublet_scores.py │ ├── run_tangram.py │ ├── run_umap.py │ ├── subtract_scrublet.py │ └── write_metadata.py ├── resources │ ├── .DS_Store │ ├── __init__.py │ ├── cell_cycle_genes.tsv │ ├── metrics_summary_col_conversion.tsv │ ├── mouse_cell_cycle_genes.tsv │ ├── qc_gene_list_mouse.csv │ ├── qc_genelist_1.0.csv │ ├── sample_file_inc_demultiplexing.txt │ ├── sample_file_qc_atac.txt │ ├── sample_file_qc_mm.txt │ ├── sample_file_qc_mm_gex_only.txt │ ├── sample_file_qc_multiome.txt │ ├── sample_file_qc_multiome_cellranger.txt │ └── sample_file_qc_spatial.txt └── version.py ├── pipeline_env.yaml ├── pyproject.toml └── tests ├── helpers.py ├── integration_1 └── pipeline.yml ├── integration_2 └── pipeline.yml ├── integration_3 └── pipeline.yml ├── pytest.ini ├── sample_caf.tsv 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