# Diagnostics for assessing genomic DNA contamination in RNA-seq data

## Documentation for package ‘gDNAx’ version 1.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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