|
|
|
|
|
|
|
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")
):
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.
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 |
Reference Manual | ||
Text | NEWS |
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 |
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 |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: