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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| 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 | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 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
Follow Installation instructions to use this package in your R session.
| Source Package | gDNAx_1.11.0.tar.gz |
| Windows Binary (x86_64) | gDNAx_1.11.0.zip |
| macOS Binary (big-sur-x86_64) | gDNAx_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | gDNAx_1.11.0.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 |