infercnv
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see infercnv.
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Bioconductor version: 3.9
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 (!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 | 1.0.4 |
| In Bioconductor since | BioC 3.9 (R-3.6) (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, 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | infercnv_1.0.4.tar.gz |
| Windows Binary | infercnv_1.0.4.zip |
| Mac OS X 10.11 (El Capitan) | infercnv_1.0.4.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 |
| Old Source Packages for BioC 3.9 | Source Archive |