compartmap

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

Bioconductor version: Release (3.17)

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("compartmap")

Higher-order chromatin inference with compartmap	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Details

biocViews	ATACSeq, Epigenetics, Genetics, RNASeq, SingleCell, Software
Version	1.18.0
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

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	compartmap_1.18.0.tar.gz
Windows Binary	compartmap_1.18.0.zip
macOS Binary (x86_64)	compartmap_1.18.0.tgz
macOS Binary (arm64)	compartmap_1.18.0.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