infercnv

DOI: 10.18129/B9.bioc.infercnv    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see infercnv.

Infer Copy Number Variation from Single-Cell RNA-Seq Data

Bioconductor version: 3.15

Using single-cell RNA-Seq expression to visualize CNV in cells.

Author: Timothy Tickle [aut], Itay Tirosh [aut], Christophe Georgescu [aut, cre], Maxwell Brown [aut], Brian Haas [aut]

Maintainer: Christophe Georgescu <cgeorges at broadinstitute.org>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("infercnv")

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("infercnv")

 

HTML	R Script	Visualizing Large-scale Copy Number Variation in Single-Cell RNA-Seq Expression Data
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bayesian, CopyNumberVariation, Genetics, GenomicVariation, HiddenMarkovModel, SingleCell, Software, StatisticalMethod, StructuralVariation, Transcriptomics, VariantDetection
Version	1.12.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 years)
License	BSD_3_clause + file LICENSE
Depends	R (>= 4.0)
Imports	graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, phyclust, Matrix, fastcluster, parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, RANN, leiden, reshape, rjags, fitdistrplus, future, foreach, doParallel, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements	JAGS 4.x.y
Enhances
URL	https://github.com/broadinstitute/inferCNV/wiki
BugReports	https://github.com/broadinstitute/inferCNV/issues
Depends On Me
Imports Me
Suggests Me	SCpubr
Links To Me
Build Report

Package Archives

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

Source Package	infercnv_1.12.0.tar.gz
Windows Binary	infercnv_1.12.0.zip (64-bit only)
macOS Binary (x86_64)	infercnv_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/infercnv
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/infercnv
Package Short Url	https://bioconductor.org/packages/infercnv/
Package Downloads Report	Download Stats