Package: gDNAx 1.11.0

Robert Castelo

gDNAx: Diagnostics for assessing genomic DNA contamination in RNA-seq data

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.

Authors:Beatriz Calvo-Serra [aut], Robert Castelo [aut, cre]

gDNAx_1.11.0.tar.gz
gDNAx_1.11.0.zip(r-4.7)gDNAx_1.11.0.zip(r-4.6)gDNAx_1.11.0.zip(r-4.5)
gDNAx_1.11.0.tgz(r-4.6-any)gDNAx_1.11.0.tgz(r-4.5-any)
gDNAx_1.11.0.tar.gz(r-4.7-any)gDNAx_1.11.0.tar.gz(r-4.6-any)
gDNAx_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gDNAx/json (API)

# Install 'gDNAx' in R:

install.packages('gDNAx', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/functionalgenomics/gdnax/issues

On BioConductor:gDNAx-1.11.0(bioc 3.24)gDNAx-1.10.0(bioc 3.23)

transcription transcriptomics rnaseq sequencing preprocessing software geneexpression coverage differentialexpression functionalgenomics splicedalignment alignment

4.90 score 2 stars 6 scripts 20 exports 93 dependencies

Last updated from:b94edc32cd. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	253
linux-devel-x86_64	NOTE	706
source / vignettes	OK	418
linux-release-x86_64	NOTE	710
macos-release-arm64	NOTE	475
macos-oldrel-arm64	NOTE	428
windows-devel	NOTE	646
windows-release	NOTE	653
windows-oldrel	NOTE	666
wasm-release	OK	201

Exports:allStrandModes classifyStrandMode filterBAMtx filterBAMtxFlag gDNAdx gDNAtx getDx getIgc getInt identifyStrandMode plot plotAlnOrigins plotFrgLength show singleEnd strandedness strandMode strandMode<-strnessByFeature testBAMtxFlag

Dependencies:abind AnnotationDbi AnnotationHub askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl DBI dbplyr DelayedArray dplyr fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges glue httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plotrix png purrr R6 rappdirs RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 VariantAnnotation vctrs withr XML XVector yaml

The gDNAx package

Rendered fromgDNAx.Rmdusingknitr::rmarkdown

Last update: 2025-04-14
Started: 2023-03-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
gDNAx: diagnostics for assessing genomic DNA contamination in RNA-seq data	gDNAx-package gDNAx
Filter alignments in a BAM file using a transcriptome	filterBAMtx filterBAMtxFlag testBAMtxFlag
Calculate gDNA diagnostics	gDNAdx plot,gDNAx,ANY-method plotAlnOrigins plotFrgLength
Remove gDNA contamination from RNA-seq data	gDNAtx
gDNAx class	allStrandModes allStrandModes,gDNAx-method gDNAx-class getDx getDx,gDNAx-method getIgc getIgc,gDNAx-method getInt getInt,gDNAx-method show show,gDNAx-method singleEnd singleEnd,gDNAx-method strandedness strandedness,gDNAx-method strandMode strandMode,gDNAx-method strandMode<- strandMode<-,gDNAx-method
Identify strandMode	classifyStrandMode identifyStrandMode strandedness,BamFileList-method strandedness,character-method strnessByFeature