infercnv

DOI: 10.18129/B9.bioc.infercnv    

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

Bioconductor version: Release (3.10)

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>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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 1.2.1
In Bioconductor since BioC 3.9 (R-3.6) (0.5 years)
License BSD_3_clause + file LICENSE
Depends R (>= 3.6)
Imports graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, Matrix, fastcluster, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, 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
Links To Me
Build Report  

Package Archives

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

Source Package infercnv_1.2.1.tar.gz
Windows Binary infercnv_1.2.1.zip
Mac OS X 10.11 (El Capitan) infercnv_1.2.1.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
Old Source Packages for BioC 3.10 Source Archive

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