.gitattributes
.gitignore
.travis.yml
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
ALLCools/__init__.py
ALLCools/__main__.py
ALLCools/_allc_to_bigwig.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/api.py
ALLCools/utilities.py
ALLCools/clustering/ConsensusClustering.py
ALLCools/clustering/__init__.py
ALLCools/clustering/art_of_tsne.py
ALLCools/clustering/balanced_knn.py
ALLCools/clustering/balanced_pca.py
ALLCools/clustering/dmg.py
ALLCools/clustering/feature_enrichment.py
ALLCools/clustering/integration.py
ALLCools/clustering/mcad.py
ALLCools/clustering/pvclust.py
ALLCools/clustering/scanorama.py
ALLCools/clustering/sccaf.py
ALLCools/clustering/scrublet.py
ALLCools/count_matrix/__init__.py
ALLCools/count_matrix/h5ad.py
ALLCools/count_matrix/mcad.py
ALLCools/count_matrix/mcds.py
ALLCools/dmr/__init__.py
ALLCools/dmr/corr.py
ALLCools/dmr/dendrogram.py
ALLCools/dmr/dmr_lineage.py
ALLCools/dmr/fimo.py
ALLCools/dmr/get_fasta.py
ALLCools/dmr/kmeans.py
ALLCools/dmr/rms_test.py
ALLCools/igv/BaseClass.py
ALLCools/igv/Session.py
ALLCools/igv/Track.py
ALLCools/igv/__init__.py
ALLCools/igv/defaults.py
ALLCools/igv/make_session.py
ALLCools/mcds/__init__.py
ALLCools/mcds/mcds.py
ALLCools/mcds/utilities.py
ALLCools/motif/__init__.py
ALLCools/motif/ame.py
ALLCools/motif/cmotif.py
ALLCools/motif/fimo.py
ALLCools/motif/motif_scan.py
ALLCools/motif/utilities.py
ALLCools/plot/__init__.py
ALLCools/plot/categorical_scatter.py
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/schema/__init__.py
ALLCools/schema/allc_schema.py
ALLCools/schema/mcds_schema.py
allcools.egg-info/PKG-INFO
allcools.egg-info/SOURCES.txt
allcools.egg-info/dependency_links.txt
allcools.egg-info/entry_points.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/logo.png
docs/allcools/references.bib
docs/allcools/.github/workflows/deploy.yml
docs/allcools/cell_level/basic/intro_basic_clustering.md
docs/allcools/cell_level/basic/mcg_5kb_basic.ipynb
docs/allcools/cell_level/basic/mch_mcg_100k_basic.ipynb
docs/allcools/cell_level/dmg/01-AddGenemCFractions.ipynb
docs/allcools/cell_level/dmg/02-DifferentiallyMethylatedGenes.ipynb
docs/allcools/cell_level/dmg/03-PlotClusterDMGs.ipynb
docs/allcools/cell_level/dmg/intro_dmg.md
docs/allcools/cell_level/doublets/doublet_score_chrom100k.ipynb
docs/allcools/cell_level/doublets/intro_doublets.md
docs/allcools/cell_level/step_by_step/intro_step_by_step_clustering.md
docs/allcools/cell_level/step_by_step/100kb/01-CellBasicFiltering.ipynb
docs/allcools/cell_level/step_by_step/100kb/02-BasicFeatureFiltering.ipynb
docs/allcools/cell_level/step_by_step/100kb/03-HighlyVariableFeatureSelection.ipynb
docs/allcools/cell_level/step_by_step/100kb/04a-PreclusteringAndClusterEnrichedFeatures-mCH.ipynb
docs/allcools/cell_level/step_by_step/100kb/04b-PreclusteringAndClusterEnrichedFeatures-mCG.ipynb
docs/allcools/cell_level/step_by_step/100kb/05-DecompositionAndEmbedding.ipynb
docs/allcools/cell_level/step_by_step/100kb/06-Clustering.ipynb
docs/allcools/img/ALLCools.svg
docs/allcools/start/installation.md
docs/allcools/start/intro.md
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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test/file/Cell02.allc.tsv.gz
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test/file/Cell05.allc.tsv.gz
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