Man pages for JunctionSeq
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
| buildAllPlots | Create and save a full battery of JunctionSeq expression... |
| buildAllPlotsForGene | Create and save one or more JunctionSeq expression plots. |
| defaultColorList | JunctionSeq Color Parameters |
| estimateEffectSizes | Estimate Effect Sizes, parameter estimates, etc. |
| estimateJunctionSeqDispersions | JunctionSeq Dispersion Estimation |
| estimateJunctionSeqSizeFactors | Estimate Size Factors |
| fitJunctionSeqDispersionFunction | Fit Shared Dispersion Function |
| JunctionSeqCountSet-class | Class '"JunctionSeqCountSet"' |
| plotDispEsts | Plot Fitted and Test-wise Dispersion |
| plotJunctionSeqResultsForGene | Generate a JunctionSeq expression plot. |
| plotMA | Generate a MA-Plot |
| readAnnotationData | Read junctionSeq annotation files produced by QoRTs. |
| readJunctionSeqCounts | Read junctionSeq count files |
| runJunctionSeqAnalyses | Run a JunctionSeq analysis. |
| setJunctionSeqCompiledSourcePackage | Set the source of the internal compiled C++ binaries. |
| testForDiffUsage | Test Junctions for Differential Junction Usage |
| writeBedTrack | Write splice junction browser tracks |
| writeCompleteResults | Produce output data files, given annotation files and DEXSeq... |
