infercnv
This is thereleased version of infercnv; for the devel version, seeinfercnv.
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("infercnv")For older versions of R, please refer to the appropriateBioconductor 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 | 1.26.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (6.5 years) |
| License | BSD_3_clause + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | infercnv_1.26.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | infercnv_1.26.0.tgz |
| macOS Binary (arm64) | infercnv_1.26.0.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 |