atacInferCnv
This is the released version of atacInferCnv; for the devel version, see atacInferCnv.
Call CNV from single cell ATAC-seq data based on InferCNV adaptation
Bioconductor version: Release (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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CopyNumberVariation, Epigenetics, ImmunoOncology, Sequencing, SingleCell, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | atacInferCnv_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | atacInferCnv_1.0.0.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 |
| Old Source Packages for BioC 3.23 | Source Archive |