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 (3.20)

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], Robert Castelo [aut, cre]

Maintainer: Robert Castelo <robert.castelo 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 1.3.1
In Bioconductor since BioC 3.18 (R-4.3) (1 year)
License Artistic-2.0
Depends R (>= 4.3)
Imports methods, BiocGenerics, BiocParallel, matrixStats, Biostrings, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, GenomicFiles, GenomicAlignments, GenomicFeatures, Rsamtools, AnnotationHub, RColorBrewer, AnnotationDbi, bitops, plotrix, SummarizedExperiment, grDevices, graphics, stats, utils, cli
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
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package gDNAx_1.3.1.tar.gz
Windows Binary gDNAx_1.3.1.zip (64-bit only)
macOS Binary (x86_64) gDNAx_1.3.1.tgz
macOS Binary (arm64) gDNAx_1.3.1.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