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>

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")

 

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

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