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.gitignore
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LICENSE
MANIFEST.in
README.md
allcools_environment.yaml
pyproject.toml
setup.py
ALLCools/__init__.py
ALLCools/__main__.py
ALLCools/_allc_to_bigwig.py
ALLCools/_allc_to_bigwig_new.py
ALLCools/_allc_to_region_count.py
ALLCools/_bam_to_allc.py
ALLCools/_doc.py
ALLCools/_extract_allc.py
ALLCools/_merge_allc.py
ALLCools/_open.py
ALLCools/_version.py
ALLCools/api.py
ALLCools/table_to_allc.py
ALLCools/utilities.py
ALLCools/clustering/ClusterMerging.py
ALLCools/clustering/ConsensusClustering.py
ALLCools/clustering/__init__.py
ALLCools/clustering/art_of_tsne.py
ALLCools/clustering/balanced_pca.py
ALLCools/clustering/dmg.py
ALLCools/clustering/incremental_pca.py
ALLCools/clustering/mcad.py
ALLCools/clustering/pvclust.py
ALLCools/clustering/doublets/__init__.py
ALLCools/clustering/doublets/coverage_doublets.py
ALLCools/clustering/doublets/scrublet.py
ALLCools/clustering/feature_selection/__init__.py
ALLCools/clustering/feature_selection/feature_enrichment.py
ALLCools/count_matrix/__init__.py
ALLCools/count_matrix/atac.py
ALLCools/count_matrix/dataset.py
ALLCools/count_matrix/h5ad.py
ALLCools/count_matrix/mcad.py
ALLCools/count_matrix/mcds.py
ALLCools/count_matrix/snap.py
ALLCools/count_matrix/zarr.py
ALLCools/dmr/__init__.py
ALLCools/dmr/call_dmr.py
ALLCools/dmr/call_dms.py
ALLCools/dmr/parse_methylpy.py
ALLCools/dmr/rms_test.py
ALLCools/integration/__init__.py
ALLCools/integration/cca.py
ALLCools/integration/confusion.py
ALLCools/integration/harmony.py
ALLCools/mcds/__init__.py
ALLCools/mcds/correlation.py
ALLCools/mcds/mcds.py
ALLCools/mcds/region_ds.py
ALLCools/mcds/utilities.py
ALLCools/motif/__init__.py
ALLCools/motif/motifs.py
ALLCools/motif/parse_meme.py
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ALLCools/plot/__init__.py
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ALLCools/plot/color.py
ALLCools/plot/continuous_scatter.py
ALLCools/plot/contour.py
ALLCools/plot/decomposition.py
ALLCools/plot/dendro.py
ALLCools/plot/interactive_scatter.py
ALLCools/plot/qc_plots.py
ALLCools/plot/size.py
ALLCools/plot/sunburst.py
ALLCools/plot/text_anno_scatter.py
ALLCools/plot/utilities.py
ALLCools/pseudo_cell/__init__.py
ALLCools/pseudo_cell/pseudo_cell_kmeans.py
ALLCools/pseudo_cell/pseudo_cell_knn.py
ALLCools/reptile/__init__.py
ALLCools/reptile/reptile.py
ALLCools/sandbox/__init__.py
ALLCools/sandbox/balanced_knn.py
ALLCools/sandbox/scanorama.py
ALLCools/sandbox/sccaf.py
ALLCools/sandbox/igv/BaseClass.py
ALLCools/sandbox/igv/Session.py
ALLCools/sandbox/igv/Track.py
ALLCools/sandbox/igv/__init__.py
ALLCools/sandbox/igv/defaults.py
ALLCools/sandbox/igv/make_session.py
ALLCools/sandbox/motif/__init__.py
ALLCools/sandbox/motif/ame.py
ALLCools/sandbox/motif/cmotif.py
ALLCools/sandbox/motif/fimo.py
ALLCools/sandbox/motif/motif_scan.py
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ALLCools/schema/__init__.py
ALLCools/schema/mcds_schema.py
allcools.egg-info/PKG-INFO
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allcools.egg-info/dependency_links.txt
allcools.egg-info/entry_points.txt
allcools.egg-info/requires.txt
allcools.egg-info/top_level.txt
docs/CONDUCT.md
docs/CONTRIBUTING.md
docs/README.md
docs/requirements.txt
docs/allcools/_config.yml
docs/allcools/_toc.yml
docs/allcools/intro.md
docs/allcools/references.bib
docs/allcools/.github/workflows/deploy.yml
docs/allcools/cell_level/basic/intro_basic_clustering.md
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docs/allcools/cell_level/dmg/03-PlotClusterDMGs.ipynb
docs/allcools/cell_level/dmg/04-PairwiseDMG.ipynb
docs/allcools/cell_level/dmg/c1.TopMarker.png
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docs/allcools/cell_level/integration/PreprocessRNA.ipynb
docs/allcools/cell_level/integration/intro_integration.md
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docs/allcools/cell_level/integration/multi_modalities/Neurons/02-preprocess_SMART.ipynb
docs/allcools/cell_level/integration/multi_modalities/Neurons/03-preprocess_snATAC.ipynb
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docs/allcools/cell_level/simulation/fraction_based_clustering.ipynb
docs/allcools/cell_level/simulation/hypo_score_based_clustering.ipynb
docs/allcools/cell_level/simulation/simulate_mcds.ipynb
docs/allcools/cell_level/step_by_step/intro_step_by_step_clustering.md
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docs/allcools/cell_level/step_by_step/100kb/05-DecompositionAndEmbedding.ipynb
docs/allcools/cell_level/step_by_step/100kb/06-Clustering.ipynb
docs/allcools/cell_level/step_by_step/100kb/07-FinalEmbeddingWithCEF.ipynb
docs/allcools/cell_level/step_by_step/100kb/intro_100kb.md
docs/allcools/cell_level/step_by_step/5kb/01-CellBasicFiltering.ipynb
docs/allcools/cell_level/step_by_step/5kb/02-DecompositionAndEmbedding.ipynb
docs/allcools/cell_level/step_by_step/5kb/03-Clustering.ipynb
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docs/allcools/cluster_level/intro.md
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docs/allcools/cluster_level/Correlation/simulate_rms.ipynb
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docs/allcools/cluster_level/REPTILE/intro_reptile.md
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test/__init__.py
test/test_allc_to_region_count.py
test/test_bam_to_allc.py
test/test_extract_allc.py
test/utilities.py
test/file/Cell01.allc.tsv.gz
test/file/Cell01.allc.tsv.gz.tbi
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