Finding differentially expressed unannotated genomic regions from RNA-seq data


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Documentation for package ‘srnadiff’ version 1.18.2

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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