infercnv

DOI:10.18129/B9.bioc.infercnv

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

Bioconductor version: Release (3.16)

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

Installation

To install this package, start R (version "4.2") 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

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("infercnv")

HTML	R Script	Visualizing Large-scale Copy Number Variation in Single-Cell RNA-Seq Expression Data
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bayesian,CopyNumberVariation,Genetics,GenomicVariation,HiddenMarkovModel,SingleCell,Software,StatisticalMethod,StructuralVariation,Transcriptomics,VariantDetection
Version	1.14.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 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
LinkingTo
Suggests	BiocStyle,knitr,rmarkdown,testthat
SystemRequirements	JAGS 4.x.y
Enhances
URL	https://github.com/broadinstitute/inferCNV/wiki
BugReports	https://github.com/broadinstitute/inferCNV/issues
Depends On Me
Imports Me
Suggests Me	SCpubr
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	infercnv_1.14.0.tar.gz
Windows Binary	infercnv_1.14.0.zip
macOS Binary (x86_64)	infercnv_1.14.0.tgz
macOS Binary (arm64)	infercnv_1.14.0.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	//www.andersvercelli.com/packages/infercnv/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive