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 (3.21)
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, cre], Erik Christensen [aut], Jonathan Wang [aut], Parisa Shooshtari [aut]
Maintainer: Arrian Gibson-Khademi <agibsonk at uwo.ca>
citation("scATAC.Explorer")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 |
Details
| biocViews | ExperimentData, ExpressionData, GEO, Genome, PackageTypeData, SequencingData, SingleCellData, Tissue |
| Version | 1.13.0 |
| 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_1.13.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (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 |