API for mzytnicki/srnadiff
Finding differentially expressed unannotated genomic regions from RNA-seq data
| Global functions | |
|---|---|
| IRlist2GR | Source code |
| annotReg | Man page |
| annotReg,srnadiffExp-method | Man page |
| annotReg<- | Man page |
| annotReg<-,srnadiffExp-method | Man page |
| bamFiles | Man page |
| bamFiles,srnadiffExp-method | Man page |
| checkParameters | Source code |
| chromosomeSizes | Man page |
| chromosomeSizes,srnadiffExp-method | Man page |
| computeLogFoldChange | Source code |
| computeNormFactors | Source code |
| computePvalues | Source code |
| countMatrix | Man page |
| countMatrix,srnadiffExp-method | Man page |
| coverages | Man page |
| coverages,srnadiffExp-method | Man page |
| cvgNormalization | Source code |
| hmm | Source code |
| normFactors | Man page |
| normFactors,srnadiffExp-method | Man page |
| normFactors<- | Man page |
| normFactors<-,srnadiffExp,numeric-method | Man page |
| parameters | Man page |
| parameters,srnadiffExp-method | Man page |
| parameters<- | Man page |
| parameters<-,srnadiffExp-method | Man page |
| plotRegions | Man page Source code |
| print.srnadiff_par | Man page Source code |
| rcpp_buildHmm | Source code |
| rcpp_ir | Source code |
| rcpp_normalization | Source code |
| rcpp_viterbi | Source code |
| readAnnotation | Man page Source code |
| reconcileRegions | Source code |
| regions | Man page |
| regions,srnadiffExp-method | Man page |
| removeRedundant | Source code |
| runHmm | Source code |
| runIR | Source code |
| runNaive | Source code |
| sampleInfo | Man page |
| sampleInfo,srnadiffExp-method | Man page |
| show,srnadiffExp-method | Man page |
| srnadiff | Man page Source code |
| srnadiff-package | Man page |
| srnadiffCore | Source code |
| srnadiffDefaultParameters | Man page |
| srnadiffExample | Man page Source code |
| srnadiffExp | Man page Source code |
| srnadiffExp-class | Man page |
| useBaySeq | Source code |
| useDESeq2 | Source code |
| useEdgeR | Source code |
