atacInferCnv

Call CNV from single cell ATAC-seq data based on InferCNV adaptation

Bioconductor version: 3.23 · Package version: 1.0.0

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.

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
Downloads rank	41
Source branch	RELEASE_3_23
biocViews	CopyNumberVariation, Epigenetics, ImmunoOncology, Sequencing, SingleCell, Software

Documentation

atacInferCnv: CNV inference from scATAC-seq data

Download

Source package

Dependencies

Depends: R (>= 4.5.0), utils

Imports: infercnv (>= 1.3.1), Signac, Seurat, GenomicRanges, GenomeInfoDb, S4Vectors, config, stringr, ggplot2, SummarizedExperiment, SingleCellExperiment, Rcpp

LinkingTo: Rcpp, RcppEigen

Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown