atacInferCnv
This is the development version of atacInferCnv; for the stable release version, see atacInferCnv.
All Bioconductor versions of atacInferCnv
3.24 (devel), 3.23 (release)
Call CNV from single cell ATAC-seq data based on InferCNV adaptation
Bioconductor version: 3.24 · Package version: 1.1.0
The package prepares input scATAC-seq data and adapts for copy number variance profiling with InferCNV package usage. It has also various paramters to control the analysis (e.g. external normal reference usage, meta-cells, bin size, etc) and custom plot visualizations.
Author: Konstantin Okonechnikov [aut, cre] 
, Supat Thongjuea [aut, fnd]
Maintainer: Konstantin Okonechnikov <k.okonechnikov at gmail.com>
Citation
From within R, enter citation("atacInferCnv"):
Konstantin Okonechnikov, Supat Thongjuea. atacInferCnv: Call CNV from single cell ATAC-seq data based on InferCNV adaptation. doi:10.18129/B9.bioc.atacInferCnv, R package version 1.1.0, https://bioconductor.org/packages/atacInferCnv.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("atacInferCnv")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.1.0 |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/kokonech/atacInferCNV |
| Bug Reports | https://github.com/kokonech/atacInferCNV/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.23 (R-4.6) (less than a year) |
| Downloads rank | 2330 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | CopyNumberVariation, Epigenetics, ImmunoOncology, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/atacInferCnv/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("atacInferCnv")| atacInferCnv: CNV inference from scATAC-seq data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | atacInferCnv_1.1.0.tar.gz |
| macOS binary (arm64) | atacInferCnv_1.1.0.tgz |
| macOS binary (x86_64) | atacInferCnv_1.1.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/atacInferCnv |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/atacInferCnv |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0), utils
Imports: infercnv (>= 1.3.1), Signac, Seurat, GenomicRanges, GenomeInfoDb, S4Vectors, config, stringr, ggplot2, SummarizedExperiment, SingleCellExperiment, Rcpp
Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown