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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
See More
| Suggests | covr, testthat, knitr, Rcpp, rmarkdown, markdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| 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 |