This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

infercnv

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

Bioconductor version: Release (3.17)

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 "4.3") 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")
Visualizing Large-scale Copy Number Variation in Single-Cell RNA-Seq Expression Data HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Bayesian, CopyNumberVariation, Genetics, GenomicVariation, HiddenMarkovModel, SingleCell, Software, StatisticalMethod, StructuralVariation, Transcriptomics, VariantDetection
Version 1.16.0
In Bioconductor since BioC 3.9 (R-3.6) (4.5 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, igraph, reshape2, rjags, fitdistrplus, future, foreach, doParallel, Seurat, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse
Linking To
Suggests BiocStyle, knitr, rmarkdown, testthat
System Requirements JAGS 4.x.y
Enhances
URL https://github.com/broadinstitute/inferCNV/wiki
Bug Reports https://github.com/broadinstitute/inferCNV/issues
See More
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_1.16.0.tar.gz
Windows Binary infercnv_1.16.0.zip
macOS Binary (x86_64) infercnv_1.16.0.tgz
macOS Binary (arm64) infercnv_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/infercnv
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/infercnv
Bioc Package Browser https://code.bioconductor.org/browse/infercnv/
Package Short Url https://bioconductor.org/packages/infercnv/
Package Downloads Report Download Stats