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compartmap

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


Bioconductor version: Release (3.18)

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 vai.org>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("compartmap")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews ATACSeq, Epigenetics, Genetics, RNASeq, SingleCell, Software
Version 1.20.0
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
System Requirements
URL https://github.com/biobenkj/compartmap
Bug Reports https://github.com/biobenkj/compartmap/issues
See More
Suggests covr, testthat, knitr, Rcpp, rmarkdown, markdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary compartmap_1.20.0.zip
macOS Binary (x86_64) compartmap_1.20.0.tgz
macOS Binary (arm64) compartmap_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/compartmap
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/compartmap
Bioc Package Browser https://code.bioconductor.org/browse/compartmap/
Package Short Url https://bioconductor.org/packages/compartmap/
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