gDNAx
Diagnostics for assessing genomic DNA contamination in RNA-seq data
Bioconductor version: Release (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("gDNAx")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, Coverage, DifferentialExpression, FunctionalGenomics, GeneExpression, Preprocessing, RNASeq, Sequencing, Software, SplicedAlignment, Transcription, Transcriptomics |
| Version | 1.4.0 |
| 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_1.4.0.tar.gz |
| Windows Binary (x86_64) | gDNAx_1.4.0.zip (64-bit only) |
| macOS Binary (x86_64) | gDNAx_1.4.0.tgz |
| macOS Binary (arm64) | gDNAx_1.4.0.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 |