gDNAx

DOI: 10.18129/B9.bioc.gDNAx  

Diagnostics for assessing genomic DNA contamination in RNA-seq data

Bioconductor version: Release (3.18)

Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.

Author: Beatriz Calvo-Serra [aut, cre], Robert Castelo [aut]

Maintainer: Beatriz Calvo-Serra <beatriz.calvo at upf.edu>

Installation

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

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

BiocManager::install("gDNAx")

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("gDNAx")

 

HTML	R Script	The gDNAx package
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, SplicedAlignment, Transcription, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	Artistic-2.0
Depends	R (>= 4.3)
Imports	methods, BiocGenerics, BiocParallel, Biostrings, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, GenomicFiles, GenomicAlignments, GenomicFeatures, Rsamtools, AnnotationHub, RColorBrewer, AnnotationDbi, bitops, plotrix, SummarizedExperiment, grDevices, graphics, stats, utils
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData
SystemRequirements
Enhances
URL	https://github.com/functionalgenomics/gDNAx
BugReports	https://github.com/functionalgenomics/gDNAx/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	gDNAx_1.0.0.tar.gz
Windows Binary	gDNAx_1.0.0.zip
macOS Binary (x86_64)	gDNAx_1.0.0.tgz
macOS Binary (arm64)	gDNAx_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gDNAx
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gDNAx
Bioc Package Browser	https://code.bioconductor.org/browse/gDNAx/
Package Short Url	https://bioconductor.org/packages/gDNAx/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive