API for jianhong/InPAS
Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
| Global functions | |
|---|---|
| $,UTR3eSet-method | Man page |
| $<-,UTR3eSet-method | Man page |
| .collapse_list | Source code |
| .onAttach | Man page Source code |
| InPAS | Man page |
| UTR3eSet | Source code |
| UTR3eSet-class | Man page |
| addChr2Exclude | Man page Source code |
| addInPASEnsDb | Man page Source code |
| addInPASGenome | Man page Source code |
| addInPASOutputDirectory | Man page Source code |
| addInPASTxDb | Man page Source code |
| addLockName | Man page Source code |
| adjust_distalCPs | Man page Source code |
| adjust_proximalCPs | Man page Source code |
| adjust_proximalCPsByNBC | Man page Source code |
| adjust_proximalCPsByPWM | Man page Source code |
| assemble_allCov | Man page Source code |
| assign_feature | Man page Source code |
| calculate_mse | Man page Source code |
| coerce,UTR3eSet,ExpressionSet-method | Man page |
| coerce,UTR3eSet,GRanges-method | Man page |
| compensation | Man page Source code |
| extract_UTR3Anno | Man page Source code |
| fft.smooth | Man page Source code |
| filter_testOut | Man page Source code |
| find_minMSEDistr | Man page Source code |
| find_valleyBySpline | Man page Source code |
| gcComp | Man page Source code |
| gcContents | Man page Source code |
| getChr2Exclude | Man page Source code |
| getInPASEnsDb | Man page Source code |
| getInPASGenome | Man page Source code |
| getInPASOutputDirectory | Man page Source code |
| getInPASSQLiteDb | Man page Source code |
| getInPASTxDb | Man page Source code |
| getLockName | Man page Source code |
| get_PAscore | Man page Source code |
| get_PAscore2 | Man page Source code |
| get_UTR3CDS | Man page Source code |
| get_UTR3TotalCov | Man page Source code |
| get_UTR3eSet | Man page Source code |
| get_UTR3region | Man page Source code |
| get_chromosomes | Man page Source code |
| get_depthWeight | Man page Source code |
| get_lastCDSUTR3 | Man page Source code |
| get_regionCov | Man page Source code |
| get_seqLen | Man page Source code |
| get_ssRleCov | Man page Source code |
| get_totalCov | Man page Source code |
| get_usage4plot | Man page Source code |
| get_zScoreCutoff | Man page Source code |
| mapComp | Man page Source code |
| parse_TxDb | Man page Source code |
| plot_utr3Usage | Man page Source code |
| polish_CPs | Man page Source code |
| remove_convergentUTR3s | Man page Source code |
| run_coverageQC | Man page Source code |
| run_fisherExactTest | Man page Source code |
| run_limmaAnalysis | Man page Source code |
| run_singleGroupAnalysis | Man page Source code |
| run_singleSampleAnalysis | Man page Source code |
| search_CPs | Man page Source code |
| search_distalCPs | Man page Source code |
| search_proximalCPs | Man page Source code |
| set_globals | Man page Source code |
| setup_CPsSearch | Man page Source code |
| setup_GSEA | Man page Source code |
| setup_parCPsSearch | Man page Source code |
| setup_sqlitedb | Man page Source code |
| show,UTR3eSet-method | Man page |
| test_dPDUI | Man page Source code |
| trim_seqnames | Man page Source code |
| utr3.mm10 | Man page |
