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Bioconductor - gDNAx (development version)

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 (3.22)

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 "4.5") 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")
Details biocViews Alignment, Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, SplicedAlignment, Transcription, Transcriptomics Version 1.7.3 In Bioconductor since BioC 3.18 (R-4.3) (1.5 years) License Artistic-2.0 Depends R (>= 4.3) Imports methods, BiocGenerics, BiocParallel, matrixStats, Biostrings, S4Vectors, IRanges, Seqinfo, 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 Package Archives

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

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