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-any)gDNAx_1.11.0.zip(r-4.6-any)gDNAx_1.11.0.zip(r-4.5-any)
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)

transcriptiontranscriptomicsrnaseqsequencingpreprocessingsoftwaregeneexpressioncoveragedifferentialexpressionfunctionalgenomicssplicedalignmentalignment

3.90 score 2 stars 8 scripts 441 downloads 20 exports 94 dependencies

Last updated from:b94edc32cd. Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING211
linux-develERROR541
source / vignettesERROR337
linux-releaseERROR448
macos-releaseERROR482
macos-oldrelERROR346
windows-develERROR427
windows-releaseERROR395
windows-oldrelERROR372
wasm-releaseOK167

Exports:allStrandModesclassifyStrandModefilterBAMtxfilterBAMtxFlaggDNAdxgDNAtxgetDxgetIgcgetIntidentifyStrandModeplotplotAlnOriginsplotFrgLengthshowsingleEndstrandednessstrandModestrandMode<-strnessByFeaturetestBAMtxFlag

Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesgluehttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplotrixpngpurrrR6rappdirsRColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
gDNAx: diagnostics for assessing genomic DNA contamination in RNA-seq datagDNAx-package gDNAx
Filter alignments in a BAM file using a transcriptomefilterBAMtx filterBAMtxFlag testBAMtxFlag
Calculate gDNA diagnosticsgDNAdx plot,gDNAx,ANY-method plotAlnOrigins plotFrgLength
Remove gDNA contamination from RNA-seq datagDNAtx
gDNAx classallStrandModes 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 strandModeclassifyStrandMode identifyStrandMode strandedness,BamFileList-method strandedness,character-method strnessByFeature