gDNAinRNAseqData

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see gDNAinRNAseqData.

RNA-seq data with different levels of gDNA contamination

Bioconductor version: 3.18

Provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554, 2022. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination.

Author: Robert Castelo [aut, cre]

Maintainer: Robert Castelo <robert.castelo at upf.edu>

Citation (from within R, enter citation("gDNAinRNAseqData")):

Installation

To install this package, start R (version "4.3") and enter:


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

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("gDNAinRNAseqData")

RNA-seq data with different levels of gDNA contamination HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, RNASeqData, SequencingData

Version 1.2.0

License Artistic-2.0

Depends R (>= 4.3)

Imports RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools

System Requirements

URL https://github.com/functionalgenomics/gDNAinRNAseqData

Bug Reports https://github.com/functionalgenomics/gDNAinRNAseqData

Suggests BiocStyle, knitr, rmarkdown

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me gDNAx

Links To Me

Build Report Build Report

Package Archives

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

Source Package gDNAinRNAseqData_1.2.0.tar.gz

Windows Binary

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/gDNAinRNAseqData

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gDNAinRNAseqData

Package Short Url https://bioconductor.org/packages/gDNAinRNAseqData/

Package Downloads Report Download Stats