gDNAx

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

Diagnostics for assessing genomic DNA contamination in RNA-seq data

Bioconductor version: 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>

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

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")

The gDNAx package HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, SplicedAlignment, Transcription, Transcriptomics

Version 1.0.2

In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)

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

Suggests BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData

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Package Archives

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

Source Package gDNAx_1.0.2.tar.gz

Windows Binary gDNAx_1.0.2.zip

macOS Binary (x86_64) gDNAx_1.0.2.tgz

macOS Binary (arm64) gDNAx_1.0.2.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