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 |