compartmap

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see compartmap.

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

Bioconductor version: 3.16

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 "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

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

Version 1.16.0

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

Suggests covr, testthat, knitr, Rcpp, rmarkdown, markdown

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Build Report Build Report

Package Archives

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

Source Package compartmap_1.16.0.tar.gz

Windows Binary compartmap_1.16.0.zip

macOS Binary (x86_64) compartmap_1.16.0.tgz

macOS Binary (arm64) compartmap_1.16.0.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 3.16 Source Archive