gDNAx
This is thereleased version of gDNAx; for the devel version, seegDNAx.
Diagnostics for assessing genomic DNA contamination in RNA-seq data
Bioconductor version: Release (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("gDNAx")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("gDNAx")For older versions of R, please refer to the appropriateBioconductor 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 | 1.8.1 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 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
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | gDNAx_1.8.1.tar.gz |
| Windows Binary (x86_64) | gDNAx_1.8.0.zip (64-bit only) |
| macOS Binary (x86_64) | gDNAx_1.8.1.tgz |
| macOS Binary (arm64) | gDNAx_1.8.1.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 |
| Old Source Packages for BioC 3.22 | Source Archive |