scATAC.Explorer

DOI: 10.18129/B9.bioc.scATAC.Explorer  

A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata

Bioconductor version: Release (3.16)

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], Parisa Shooshtari [aut]

Maintainer: Arrian Gibson-Khademi <agibsonk at uwo.ca>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

HTML	R Script	scATAC.Explorer
PDF		Reference Manual
Text		NEWS

Details

biocViews	ExperimentData, ExpressionData, GEO, Genome, PackageTypeData, SequencingData, SingleCellData, Tissue
Version	1.4.0
License	Artistic-2.0
Depends	R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table, utils, S4Vectors
Imports	methods, Matrix
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL
BugReports	https://github.com/shooshtarilab/scATACseq/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scATAC.Explorer_1.4.0.tar.gz
Windows Binary
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