| 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 |