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This is the development version of infercnv; for the stable release version, see infercnv.

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

Bioconductor version: Development (3.20)

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>

Citation (from within R, enter citation("infercnv")):


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if (!require("BiocManager", quietly = TRUE))

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To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Bayesian, CopyNumberVariation, Genetics, GenomicVariation, HiddenMarkovModel, SingleCell, Software, StatisticalMethod, StructuralVariation, Transcriptomics, VariantDetection
Version 1.21.0
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, 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
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