compartmap

DOI: 10.18129/B9.bioc.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>

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

PDF		Reference Manual

Details

biocViews	ATACSeq, Epigenetics, Genetics, RNASeq, SingleCell, Software
Version	1.20.0
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
LinkingTo
Suggests	covr, testthat, knitr, Rcpp, rmarkdown, markdown
SystemRequirements
Enhances
URL	https://github.com/biobenkj/compartmap
BugReports	https://github.com/biobenkj/compartmap/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive