# Finding differentially expressed unannotated genomic regions from RNA-seq data

## Documentation for package ‘srnadiff’ version 1.11.0

- 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