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gDNAx

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

Diagnostics for assessing genomic DNA contamination in RNA-seq data


Bioconductor version: Development (3.19)

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>

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

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("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")
The gDNAx package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, SplicedAlignment, Transcription, Transcriptomics
Version 1.1.3
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
System Requirements
URL https://github.com/functionalgenomics/gDNAx
Bug Reports https://github.com/functionalgenomics/gDNAx/issues
See More
Suggests BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package gDNAx_1.1.3.tar.gz
Windows Binary gDNAx_1.1.3.zip
macOS Binary (x86_64) gDNAx_1.1.3.tgz
macOS Binary (arm64) gDNAx_1.1.0.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