LICENSE
README.md
pyproject.toml
panpipes/__init__.py
panpipes/entry.py
panpipes/funcs.py
panpipes/version.py
panpipes.egg-info/PKG-INFO
panpipes.egg-info/SOURCES.txt
panpipes.egg-info/dependency_links.txt
panpipes.egg-info/entry_points.txt
panpipes.egg-info/requires.txt
panpipes.egg-info/top_level.txt
panpipes/R_scripts/__init__.py
panpipes/R_scripts/install_R_libs.R
panpipes/R_scripts/plotQC.R
panpipes/R_scripts/plot_cluster_metrics.R
panpipes/R_scripts/plot_metrics.R
panpipes/R_scripts/plotclustree.R
panpipes/R_scripts/produce_barplot_10xmetric.v3.R
panpipes/R_scripts/refmap_wnn.R
panpipes/funcs/__init__.py
panpipes/funcs/io.py
panpipes/funcs/plotting.py
panpipes/funcs/processing.py
panpipes/funcs/scmethods.py
panpipes/panpipes/__init__.py
panpipes/panpipes/pipeline_clustering.py
panpipes/panpipes/pipeline_deconvolution_spatial.py
panpipes/panpipes/pipeline_ingest.py
panpipes/panpipes/pipeline_integration.py
panpipes/panpipes/pipeline_preprocess.py
panpipes/panpipes/pipeline_preprocess_spatial.py
panpipes/panpipes/pipeline_qc_spatial.py
panpipes/panpipes/pipeline_refmap.py
panpipes/panpipes/pipeline_vis.py
panpipes/panpipes/pipeline_clustering/pipeline.yml
panpipes/panpipes/pipeline_deconvolution_spatial/pipeline.yml
panpipes/panpipes/pipeline_ingest/pipeline.yml
panpipes/panpipes/pipeline_integration/pipeline.yml
panpipes/panpipes/pipeline_preprocess/pipeline.yml
panpipes/panpipes/pipeline_preprocess_spatial/pipeline.yml
panpipes/panpipes/pipeline_qc_spatial/pipeline.yml
panpipes/panpipes/pipeline_refmap/pipeline.yml
panpipes/panpipes/pipeline_vis/pipeline.yml
panpipes/python_scripts/__init__.py
panpipes/python_scripts/aggregate_cellranger_summary_metrics.py
panpipes/python_scripts/aggregate_csvs.py
panpipes/python_scripts/assess_background.py
panpipes/python_scripts/batch_correct_bbknn.py
panpipes/python_scripts/batch_correct_combat.py
panpipes/python_scripts/batch_correct_harmony.py
panpipes/python_scripts/batch_correct_merge.py
panpipes/python_scripts/batch_correct_mofa.py
panpipes/python_scripts/batch_correct_multivi.py
panpipes/python_scripts/batch_correct_none.py
panpipes/python_scripts/batch_correct_scanorama.py
panpipes/python_scripts/batch_correct_scvi.py
panpipes/python_scripts/batch_correct_totalvi.py
panpipes/python_scripts/batch_correct_wnn.py
panpipes/python_scripts/collate_mdata.py
panpipes/python_scripts/concat_adata.py
panpipes/python_scripts/downsample.py
panpipes/python_scripts/generate_cellxgene.py
panpipes/python_scripts/integrate_wnn.py
panpipes/python_scripts/make_adata_from_csv.py
panpipes/python_scripts/make_mudataspatial_from_csv.py
panpipes/python_scripts/plot_atac_qc.py
panpipes/python_scripts/plot_cluster_umaps.py
panpipes/python_scripts/plot_custom_markers.py
panpipes/python_scripts/plot_custom_markers_umap.py
panpipes/python_scripts/plot_features_scatter.py
panpipes/python_scripts/plot_pca.py
panpipes/python_scripts/plot_qc_spatial.py
panpipes/python_scripts/plot_scanpy_markers.py
panpipes/python_scripts/plot_umaps_batch_correct.py
panpipes/python_scripts/plot_variables_umaps.py
panpipes/python_scripts/refmap_generatescanvi.py
panpipes/python_scripts/refmap_plot_umaps.py
panpipes/python_scripts/refmap_scib.py
panpipes/python_scripts/refmap_scvitools.py
panpipes/python_scripts/rerun_find_neighbors_for_clustering.py
panpipes/python_scripts/run_cell2location.py
panpipes/python_scripts/run_clustering.py
panpipes/python_scripts/run_collate_mtd_files.py
panpipes/python_scripts/run_differential_peaks_ATAC.py
panpipes/python_scripts/run_dsb_clr.py
panpipes/python_scripts/run_filter.py
panpipes/python_scripts/run_filter_spatial.py
panpipes/python_scripts/run_find_markers.py
panpipes/python_scripts/run_find_markers_multi.py
panpipes/python_scripts/run_find_neighbors.py
panpipes/python_scripts/run_lisi.py
panpipes/python_scripts/run_preprocess_atac.py
panpipes/python_scripts/run_preprocess_prot.py
panpipes/python_scripts/run_preprocess_rna.py
panpipes/python_scripts/run_preprocess_spatial.py
panpipes/python_scripts/run_scanpyQC_atac.py
panpipes/python_scripts/run_scanpyQC_prot.py
panpipes/python_scripts/run_scanpyQC_rep.py
panpipes/python_scripts/run_scanpyQC_rna.py
panpipes/python_scripts/run_scanpyQC_spatial.py
panpipes/python_scripts/run_scib_metrics.py
panpipes/python_scripts/run_scrublet_scores.py
panpipes/python_scripts/run_umap.py
panpipes/python_scripts/subtract_scrublet.py
panpipes/python_scripts/write_metadata.py
panpipes/resources/__init__.py
panpipes/resources/cell_cycle_genes.tsv
panpipes/resources/metrics_summary_col_conversion.tsv
panpipes/resources/qc_genelist_1.0.csv
panpipes/resources/sample_file_inc_demultiplexing.txt
panpipes/resources/sample_file_qc_atac.txt
panpipes/resources/sample_file_qc_mm.txt
panpipes/resources/sample_file_qc_mm_gex_only.txt
panpipes/resources/sample_file_qc_multiome.txt
panpipes/resources/sample_file_qc_multiome_cellranger.txt
panpipes/resources/sample_file_qc_spatial.txt
tests/test_anndata.py
tests/test_ingest_funcs.py
tests/test_processing.py