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Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seq

Bioconductor version: Release (3.19)

Compartmap performs direct inference of higher-order chromatin from scRNA-seq and scATAC-seq. This package implements a James-Stein estimator for computing single-cell level higher-order chromatin domains. Further, we utilize random matrix theory as a method to de-noise correlation matrices to achieve a similar "plaid-like" patterning as observed in Hi-C and scHi-C data.

Author: Benjamin Johnson [aut, cre], Tim Triche [aut], Hui Shen [aut], Kasper Hansen [aut], Jean-Philippe Fortin [aut]

Maintainer: Benjamin Johnson <ben.johnson at>

Citation (from within R, enter citation("compartmap")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


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Reference Manual PDF


biocViews ATACSeq, Epigenetics, Genetics, RNASeq, SingleCell, Software
Version 1.22.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.1.0), SummarizedExperiment, RaggedExperiment, BiocSingular, HDF5Array
Imports GenomicRanges, parallel, grid, ggplot2, reshape2, scales, DelayedArray, rtracklayer, DelayedMatrixStats, Matrix, RMTstat
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