Package: gDNAx 1.5.0
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:
gDNAx_1.5.0.tar.gz
gDNAx_1.5.0.zip(r-4.5)gDNAx_1.5.0.zip(r-4.4)gDNAx_1.5.0.zip(r-4.3)
gDNAx_1.5.0.tgz(r-4.4-any)gDNAx_1.5.0.tgz(r-4.3-any)
gDNAx_1.5.0.tar.gz(r-4.5-noble)gDNAx_1.5.0.tar.gz(r-4.4-noble)
gDNAx_1.5.0.tgz(r-4.4-emscripten)gDNAx_1.5.0.tgz(r-4.3-emscripten)
gDNAx.pdf |gDNAx.html✨
gDNAx/json (API)
NEWS
| # 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-1.5.0(bioc 3.21)gDNAx-1.4.0(bioc 3.20)
transcriptiontranscriptomicsrnaseqsequencingpreprocessingsoftwaregeneexpressioncoveragedifferentialexpressionfunctionalgenomicssplicedalignmentalignment
Last updated 2 months agofrom:7191379bea. Checks:OK: 1 NOTE: 4 WARNING: 1 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 21 2024 |
| R-4.5-win | NOTE | Nov 21 2024 |
| R-4.5-linux | NOTE | Dec 21 2024 |
| R-4.4-win | NOTE | Nov 21 2024 |
| R-4.4-mac | NOTE | Dec 21 2024 |
| R-4.3-win | ERROR | Nov 21 2024 |
| R-4.3-mac | WARNING | Dec 21 2024 |
Exports:allStrandModesclassifyStrandModefilterBAMtxfilterBAMtxFlaggDNAdxgDNAtxgetDxgetIgcgetIntidentifyStrandModeplotplotAlnOriginsplotFrgLengthshowsingleEndstrandednessstrandModestrandMode<-strnessByFeaturetestBAMtxFlag
Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrplotrixpngpurrrR6rappdirsRColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLXVectoryamlzlibbioc
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 |
