infercnv

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see infercnv.

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

Bioconductor version: 3.13

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, CopyNumberVariation, Genetics, GenomicVariation, HiddenMarkovModel, SingleCell, Software, StatisticalMethod, StructuralVariation, Transcriptomics, VariantDetection

Version 1.8.1

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, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, RANN, leiden, reshape, rjags, fitdistrplus, future, foreach, doParallel, 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

Suggests BiocStyle, knitr, rmarkdown, testthat

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