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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 (3.20)

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 "4.4") 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 PDF
NEWS Text

Details

biocViews ExperimentData, ExpressionData, GEO, Genome, PackageTypeData, SequencingData, SingleCellData, Tissue
Version 1.11.0
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
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_1.11.0.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