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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 (3.19)

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 vai.org>

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

Installation

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

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 1.21.0
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 compartmap_1.21.0.tar.gz
Windows Binary compartmap_1.21.1.zip
macOS Binary (x86_64) compartmap_1.21.1.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/
Package Downloads Report Download Stats