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infercnv

This is the development version of infercnv; for the stable release version, see infercnv.

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.19.1
In Bioconductor since BioC 3.9 (R-3.6) (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
System Requirements JAGS 4.x.y
URL https://github.com/broadinstitute/inferCNV/wiki
Bug Reports https://github.com/broadinstitute/inferCNV/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat
Linking To
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Depends On Me
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Suggests Me SCpubr
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Build Report Build Report

Package Archives

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

Source Package infercnv_1.19.1.tar.gz
Windows Binary infercnv_1.19.1.zip
macOS Binary (x86_64) infercnv_1.19.1.tgz
macOS Binary (arm64) infercnv_1.19.1.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