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compartmap

This is the development version of compartmap; for the stable release version, see compartmap.

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

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.19.0
In Bioconductor since BioC 3.8 (R-3.5) (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
Linking To
Suggests covr, testthat, knitr, Rcpp, rmarkdown, markdown
System Requirements
Enhances
URL https://github.com/biobenkj/compartmap
Bug Reports https://github.com/biobenkj/compartmap/issues
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Build Report  

Package Archives

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

Source Package
Windows Binary compartmap_1.19.0.zip
macOS Binary (x86_64) compartmap_1.19.0.tgz
macOS Binary (arm64)
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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