API for functionalgenomics/atena
Analysis of Transposable Elements
| Global functions | |
|---|---|
| .OCTFTA_parser | Source code |
| .adjustalnmultiovTE | Source code |
| .adjustcommonTEgene | Source code |
| .appendHits | Source code |
| .atEMstep | Source code |
| .atEstep | Source code |
| .atFixedPointFun | Source code |
| .atMstepPi | Source code |
| .atMstepTheta | Source code |
| .builDictionary | Source code |
| .builDictionary_at | Source code |
| .buildOvAlignmentsMatrix | Source code |
| .buildOvValuesMatrix | Source code |
| .checkBamFileListArgs | Source code |
| .checkBamReadMapper | Source code |
| .checkEquivalentLTR | Source code |
| .checkOvandsaln | Source code |
| .checkPhenodata | Source code |
| .checkPriors | Source code |
| .checkreassignModes | Source code |
| .consolidateFeatures | Source code |
| .correctForTxEffectiveLength | Source code |
| .correctPreference | Source code |
| .correctPreferenceTS | Source code |
| .countMultiReadsGenes | Source code |
| .countUniqueRead | Source code |
| .countbymatrix | Source code |
| .createColumnData | Source code |
| .ervmapGetCounts | Source code |
| .ervmapQuantExpress | Source code |
| .factoraggregateby | Source code |
| .fetchAnnotationsFromObject | Source code |
| .fetchNHtag | Source code |
| .fetchNMtag | Source code |
| .filterNonTEs | Source code |
| .filterReadIDs | Source code |
| .filteralnreads | Source code |
| .findSuboptAlignScore | Source code |
| .findingEquivalences | Source code |
| .getAlignmentASScoreTS | Source code |
| .getAlignmentLength | Source code |
| .getAlignmentMismatches | Source code |
| .getAlignmentQueryWidth | Source code |
| .getAlignmentSumClipping | Source code |
| .getAlignmentTagScore | Source code |
| .getAlnreadids | Source code |
| .getAveLen | Source code |
| .getConsLength | Source code |
| .getFulllength_Partial_ERVs | Source code |
| .getFuzzyEquivalences | Source code |
| .getMaskUniqueAln | Source code |
| .getNoFeatureOv | Source code |
| .getOverlapLength | Source code |
| .getReadFunction | Source code |
| .getRelLength | Source code |
| .getScanBamFlag_ts | Source code |
| .getScanBamFlag_tt | Source code |
| .get_tags_in_BAM_pairedend | Source code |
| .get_tags_in_BAM_singleend | Source code |
| .getavtags | Source code |
| .getreadsdiscard | Source code |
| .getsoatag | Source code |
| .groupGeneExons | Source code |
| .joinTEsGenes | Source code |
| .matchSeqinfo | Source code |
| .mergeCloseFeatures | Source code |
| .mergeCloseFeatures_at | Source code |
| .multiNofeature | Source code |
| .onLoad | Source code |
| .pass2Filters | Source code |
| .pass3Filter | Source code |
| .pprintnames | Source code |
| .processFeatures | Source code |
| .processMultiNofeature | Source code |
| .processPriors | Source code |
| .qtex_atena | Source code |
| .qtex_ervmap | Source code |
| .qtex_telescope | Source code |
| .qtex_tetranscripts | Source code |
| .reassign | Source code |
| .reconstructERVs | Source code |
| .reconstructERVs_at | Source code |
| .reconstructTEs | Source code |
| .reconstructTEs_at | Source code |
| .rescaleAS | Source code |
| .rescaleASat | Source code |
| .secondaryAlignmentMask | Source code |
| .setBamFlags | Source code |
| .simplifyNameSearch | Source code |
| .soasAvail | Source code |
| .splitNonContinous | Source code |
| .splitNonContinous_at | Source code |
| .suboptimalAlignmentFilteringCounts | Source code |
| .summarizeCounts | Source code |
| .tsEMstep | Source code |
| .tsEstep | Source code |
| .tsFixedPointFun | Source code |
| .tsMstepPi | Source code |
| .tsMstepTheta | Source code |
| .tssummarizeCounts | Source code |
| .ttEMstep | Source code |
| .ttEstep | Source code |
| .ttFixedPointFun | Source code |
| .ttLlh | Source code |
| .ttMstep | Source code |
| .ttQuantExpress | Source code |
| ERVmapParam | Man page Source code |
| ERVmapParam-class | Man page |
| OneCodeToFindThemAll | Man page Source code |
| QuantifyParam-class | Man page |
| TEtranscriptsParam | Man page Source code |
| TEtranscriptsParam-class | Man page |
| TelescopeParam | Man page Source code |
| TelescopeParam-class | Man page |
| annotaTEs | Man page Source code |
| annotateTEsGetters | Man page |
| atena | Man page |
| atena-package | Man page |
| atenaParam | Man page Source code |
| atenaParam-class | Man page |
| features,QuantifyParam-method | Man page |
| getDNAtransposons | Man page Source code |
| getLINEs | Man page Source code |
| getLTRs | Man page Source code |
| getSINEs | Man page Source code |
| ovIntersectionStrict | Man page Source code |
| ovUnion | Man page Source code |
| path,QuantifyParam-method | Man page |
| qtex | Man page |
| qtex,AtenaParam-method | Man page |
| qtex,ERVmapParam-method | Man page |
| qtex,TEtranscriptsParam-method | Man page |
| qtex,TelescopeParam-method | Man page |
| qtex,atenaParam-method | Man page |
| rmskatenaparser | Man page Source code |
| rmskbasicparser | Man page Source code |
| rmskidentity | Man page Source code |
| show,ERVmapParam-method | Man page |
| show,TEtranscriptsParam-method | Man page |
| show,TelescopeParam-method | Man page |
| show,atenaParam-method | Man page |
