scATAC.Explorer

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scATAC.Explorer.

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

Bioconductor version: 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>

Citation (from within R, enter citation("scATAC.Explorer")):

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")

scATAC.Explorer HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

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

System Requirements

URL

Bug Reports https://github.com/shooshtarilab/scATACseq/issues

Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

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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/

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