atacInferCnv
Call CNV from single cell ATAC-seq data based on InferCNV adaptation
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("atacInferCnv")Details
| Maintainer | Konstantin Okonechnikov <k.okonechnikov@gmail.com> |
| Author | Konstantin Okonechnikov [aut, cre] (ORCID: <https://orcid.org/0000-0002-3409-2340>), Supat Thongjuea [aut, fnd] |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/kokonech/atacInferCNV |
| Bug Reports | https://github.com/kokonech/atacInferCNV/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | CopyNumberVariation, Epigenetics, ImmunoOncology, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/atacInferCnv/ |
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 1.0.0, https://bioconductor.org/packages/atacInferCnv.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | atacInferCnv_1.0.0.tar.gz |
| macOS binary (arm64) | atacInferCnv_1.0.0.tgz |
| macOS binary (x86_64) | atacInferCnv_1.0.0.tgz |
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