Finding differentially expressed unannotated genomic regions from RNA-seq data

---

Documentation for package ‘srnadiff’ version 1.18.2

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

Help Pages

srnadiff-package	Finding differentially expressed unannotated genomic regions from RNA-seq data
annotReg	Accessors for the 'annotReg' slot of an srnadiffExp object
annotReg-method	Accessors for the 'annotReg' slot of an srnadiffExp object
annotReg<-	Accessors for the 'annotReg' slot of an srnadiffExp object
annotReg<--method	Accessors for the 'annotReg' slot of an srnadiffExp object
bamFiles	Accessors for the 'bamFiles' slot of an srnadiffExp object
bamFiles-method	Accessors for the 'bamFiles' slot of an srnadiffExp object
chromosomeSizes	Accessors for the 'chromosomeSizes' slot of an srnadiffExp object
chromosomeSizes-method	Accessors for the 'chromosomeSizes' slot of an srnadiffExp object
countMatrix	Accessors for the 'countMatrix' slot of an srnadiffExp object
countMatrix-method	Accessors for the 'countMatrix' slot of an srnadiffExp object
coverages	Accessors for the 'coverages' slot of an srnadiffExp object
coverages-method	Accessors for the 'coverages' slot of an srnadiffExp object
normFactors	Accessors for the 'normFactors' slot of an srnadiffExp object
normFactors-method	Accessors for the 'normFactors' slot of an srnadiffExp object
normFactors<-	Accessors for the 'normFactors' slot of an srnadiffExp object
normFactors<--method	Accessors for the 'normFactors' slot of an srnadiffExp object
parameters	Accessors for the 'parameters' slot of an srnadiffExp object
parameters-method	Accessors for the 'parameters' slot of an srnadiffExp object
parameters<-	Accessors for the 'parameters' slot of an srnadiffExp object
parameters<--method	Accessors for the 'parameters' slot of an srnadiffExp object
plotRegions	Plot the coverage information surrounding genomic regions
print.srnadiff_par	Accessors for the 'parameters' slot of an srnadiffExp object
readAnnotation	Reads and parses GFF/GTF files
regions	Extracts differentially expressed regions of an srnadiffExp object
regions-method	Extracts differentially expressed regions of an srnadiffExp object
sampleInfo	Accessors for the 'sampleInfo' slot of an srnadiffExp object
sampleInfo-method	Accessors for the 'sampleInfo' slot of an srnadiffExp object
show-method	Infrastructure for sRNA-Seq experiment and differential expression
srnadiff	Finding differentially expressed unannotated genomic regions from RNA-seq data
srnadiffDefaultParameters	List of srnadiff default parameters.
srnadiffExample	Example constructor
srnadiffExp	Infrastructure for sRNA-Seq experiment and differential expression
srnadiffExp-class	Infrastructure for sRNA-Seq experiment and differential expression