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Diagnostics for assessing genomic DNA contamination in RNA-seq data

Bioconductor version: Release (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], Robert Castelo [aut, cre]

Maintainer: Robert Castelo <robert.castelo at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

The gDNAx package HTML R Script
Reference Manual PDF


biocViews Alignment, Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, SplicedAlignment, Transcription, Transcriptomics
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
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
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Suggests BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData
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Follow Installation instructions to use this package in your R session.

Source Package gDNAx_1.2.0.tar.gz
Windows Binary
macOS Binary (x86_64) gDNAx_1.2.0.tgz
macOS Binary (arm64) gDNAx_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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