| AdjustBatch | AdjustBatch |
| annotatetranscript | Title |
| CheckBatch | CheckBatch |
| Compare2Pos | Compare2Pos |
| convertbam2bed | convertbam2bed |
| convert.z.score | Title |
| DEAnalysisAdjustByBatch | DEAnalysisAdjustByBatch |
| FilterTranscripts | FilterTranscripts |
| gaoidtransform | Title |
| getcounts | getcounts |
| getcountsfromMatchedbed | getcountsfromMatchedbed |
| InstallRequiredPackage | InstallRequiredPackage |
| Loadlibrary | Loadlibrary |
| matchbed2annotation | matchbed2annotation |
| MatchTxs2Gene.R | MatchTxs2Gene |
| NormalizedCount | Title |
| norm_factors | Title |
| parserAnnotationFile | parserAnnotationFile |
| parserreadfiles | parserreadfiles |
| ProcessOutputFilesFrom3UTR | ProcessOutputFilesFrom3UTR |
| ProcessOutputFilesFrom3UTR_recount | ProcessOutputFilesFrom3UTR_recount |
| ProcessOutputFilesFrom5Cases | ProcessOutputFilesFrom5Cases |
| ProcessOutputFilesFromDoGsOnly | ProcessOutputFilesFromDoGsOnly |
| ProcessTranscript2 | ProcessTranscript2 |
| ReadGeneList | Title |
| ReformatTxsGene | ReformatTxsGene |
| TestUseLongestTxsOfGene | TestUseLongestTxsOfGene |
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