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gDNAinRNAseqData

This is the development version of gDNAinRNAseqData; for the stable release version, see gDNAinRNAseqData.

RNA-seq data with different levels of gDNA contamination


Bioconductor version: Development (3.20)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, RNASeqData, SequencingData
Version 1.5.0
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
See More
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_1.5.0.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/
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