GET STARTED
CELLULAR ANALYSIS
GENOMIC ANALYSIS
COMMAND LINE TOOLS
allcools allc
allcools standard
allcools profile
allcools tbi
allcools merge
allcools extract
allcools bw
allcools region
allcools generate-dataset
allcools mcds
allcools mcad
API
ALLCools
ALLCools.abc
ALLCools.abc.abc_score
ALLCools.clustering
ALLCools.clustering.doublets
ALLCools.clustering.doublets.coverage_doublets
ALLCools.clustering.doublets.scrublet
ALLCools.clustering.feature_selection
ALLCools.clustering.feature_selection.feature_enrichment
ALLCools.clustering.feature_selection.gene_panel_design
ALLCools.clustering.ClusterMerging
ALLCools.clustering.ConsensusClustering
ALLCools.clustering.art_of_tsne
ALLCools.clustering.balanced_pca
ALLCools.clustering.dmg
ALLCools.clustering.incremental_pca
ALLCools.clustering.mcad
ALLCools.clustering.pvclust
ALLCools.count_matrix
ALLCools.count_matrix.atac
ALLCools.count_matrix.dataset
ALLCools.count_matrix.h5ad
ALLCools.count_matrix.mcad
ALLCools.count_matrix.mcds
ALLCools.count_matrix.snap
ALLCools.count_matrix.zarr
ALLCools.dmr
ALLCools.dmr.call_dmr
ALLCools.dmr.call_dms
ALLCools.dmr.parse_methylpy
ALLCools.dmr.rms_test
ALLCools.gtf
ALLCools.gtf.Gtf
ALLCools.gtf.utilities
ALLCools.integration
ALLCools.integration.cca
ALLCools.integration.confusion
ALLCools.integration.harmony
ALLCools.mcds
ALLCools.mcds.correlation
ALLCools.mcds.mcds
ALLCools.mcds.region_ds
ALLCools.mcds.utilities
ALLCools.motif
ALLCools.motif.default_motif_set
ALLCools.motif.motifs
ALLCools.motif.parse_meme
ALLCools.motif.snakemake
ALLCools.plot
ALLCools.plot.genome_track
ALLCools.plot.genome_track.GtfTrack
ALLCools.plot.genome_track.HiCMatrixCoolTrack
ALLCools.plot.genome_track._pygenometrack
ALLCools.plot.categorical_scatter
ALLCools.plot.color
ALLCools.plot.continuous_scatter
ALLCools.plot.contour
ALLCools.plot.decomposition
ALLCools.plot.dendro
ALLCools.plot.interactive_scatter
ALLCools.plot.qc_plots
ALLCools.plot.size
ALLCools.plot.sunburst
ALLCools.plot.text_anno_scatter
ALLCools.plot.utilities
ALLCools.pseudo_cell
ALLCools.pseudo_cell.pseudo_cell_kmeans
ALLCools.pseudo_cell.pseudo_cell_knn
ALLCools.reptile
ALLCools.reptile.reptile
ALLCools.sandbox
ALLCools.sandbox.igv
ALLCools.sandbox.igv.BaseClass
ALLCools.sandbox.igv.Session
ALLCools.sandbox.igv.Track
ALLCools.sandbox.igv.defaults
ALLCools.sandbox.igv.make_session
ALLCools.sandbox.motif
ALLCools.sandbox.motif.ame
ALLCools.sandbox.motif.cmotif
ALLCools.sandbox.motif.fimo
ALLCools.sandbox.motif.motif_scan
ALLCools.sandbox.motif.utilities
ALLCools.sandbox.balanced_knn
ALLCools.sandbox.scanorama
ALLCools.sandbox.sccaf
ALLCools.schema
ALLCools.schema.mcds_schema
ALLCools.__main__
ALLCools._allc_to_bigwig
ALLCools._allc_to_bigwig_new
ALLCools._allc_to_region_count
ALLCools._bam_to_allc
ALLCools._doc
ALLCools._extract_allc
ALLCools._merge_allc
ALLCools._open
ALLCools._version
ALLCools.api
ALLCools.table_to_allc
ALLCools.utilities
PROJECT INFO
previous
Perform Cross-Modality Integration
next
Calculate Cell Doublet Score
