atacInferCnv
This is the development version of atacInferCnv; to use it, please install the devel version of Bioconductor.
Call CNV from single cell ATAC-seq data based on InferCNV adaptation
Bioconductor version: Development (3.23)
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("atacInferCnv")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("atacInferCnv")
For older versions of R, please refer to the appropriate Bioconductor release.
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 |
Details
| biocViews | CopyNumberVariation, Epigenetics, ImmunoOncology, Sequencing, SingleCell, Software |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.6.0), utils |
| Imports | infercnv(>= 1.3.1), Signac, Seurat, GenomicRanges, GenomeInfoDb, S4Vectors, config, stringr, ggplot2, SummarizedExperiment, SingleCellExperiment, Rcpp |
| System Requirements | |
| URL | https://github.com/kokonech/atacInferCNV |
| Bug Reports | https://github.com/kokonech/atacInferCNV/issues |
See More
| Suggests | testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown |
| Linking To | Rcpp, RcppEigen |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | atacInferCnv_0.99.7.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | atacInferCnv_0.99.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/atacInferCnv |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/atacInferCnv |
| Bioc Package Browser | https://code.bioconductor.org/browse/atacInferCnv/ |
| Package Short Url | https://bioconductor.org/packages/atacInferCnv/ |
| Package Downloads Report | Download Stats |