infercnv
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Bioconductor version: Release (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")
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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Bayesian, CopyNumberVariation, Genetics, GenomicVariation, HiddenMarkovModel, SingleCell, Software, StatisticalMethod, StructuralVariation, Transcriptomics, VariantDetection |
Version | 1.20.0 |
In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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 | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | SCpubr |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | infercnv_1.20.0.tar.gz |
Windows Binary | infercnv_1.20.0.zip |
macOS Binary (x86_64) | infercnv_1.20.0.tgz |
macOS Binary (arm64) | infercnv_1.20.0.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 |