scATAC.Explorer
This is the development version of scATAC.Explorer; for the stable release version, see scATAC.Explorer.
A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata
Bioconductor version: Development (3.24)
This package provides a tool to search and download a collection of publicly available single cell ATAC-seq datasets and their metadata. scATAC-Explorer aims to act as a single point of entry for users looking to study single cell ATAC-seq data. Users can quickly search available datasets using the metadata table and download datasets of interest for immediate analysis within R.
Author: Arrian Gibson-Khademi [aut], Erik Christensen [aut], Jonathan Wang [aut, cre], Parisa Shooshtari [aut]
Maintainer: Jonathan Wang <jwan2633 at uwo.ca>
citation("scATAC.Explorer")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scATAC.Explorer")
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("scATAC.Explorer")| scATAC.Explorer | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExpressionData, GEO, Genome, PackageTypeData, SequencingData, SingleCellData, Tissue |
| Version | 1.19.0 |
| License | Artistic-2.0 |
| Depends | R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table, utils, S4Vectors, zellkonverter |
| Imports | methods, Matrix |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/shooshtarilab/scATACseq/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| 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 | scATAC.Explorer_1.19.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/scATAC.Explorer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scATAC.Explorer |
| Package Short Url | https://bioconductor.org/packages/scATAC.Explorer/ |
| Package Downloads Report | Download Stats |