compartmap

DOI: 10.18129/B9.bioc.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 (3.14)

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 "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews ATACSeq, Epigenetics, Genetics, RNASeq, SingleCell, Software
Version 1.11.0
In Bioconductor since BioC 3.8 (R-3.5) (3 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 compartmap_1.11.0.tar.gz
Windows Binary compartmap_1.11.0.zip
macOS 10.13 (High Sierra) compartmap_1.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/compartmap
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/compartmap
Package Short Url https://bioconductor.org/packages/compartmap/
Package Downloads Report Download Stats

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