API for haowulab/TRESS
Toolbox for mRNA epigenetics sequencing analysis
| Global functions | |
|---|---|
| Basal | Man page |
| BgMethylevel | Source code |
| CallCandidates | Man page Source code |
| CallDMRs.paramEsti | Man page Source code |
| CallPeaks.multiRep | Man page Source code |
| CallPeaks.oneRep | Man page Source code |
| CallPeaks.paramEsti | Man page Source code |
| ChisqTest | Source code |
| CoefName | Man page Source code |
| CovR.parallel | Source code |
| DMRInfer | Man page Source code |
| DMR_M3vsWT | Man page |
| DMR_SixWeekvsTwoWeek | Man page |
| DivideBins | Man page Source code |
| E.Hessian.NB | Source code |
| E.d2L.R2 | Source code |
| E.d2L.Rphi | Source code |
| E.d2L.Rtheta | Source code |
| E.d2L.phi2 | Source code |
| E.d2L.phitheta | Source code |
| E.d2L.theta2 | Source code |
| EstiMu | Source code |
| EstiPhi | Source code |
| EstiPhi.IterativeUpdate | Source code |
| EstiPhi.JointUpdate | Source code |
| EstiPhi.SingleUpdate | Source code |
| EstiVarofMu | Source code |
| Fisher.R | Source code |
| Grad.NB | Source code |
| Hessian.NB | Source code |
| JProfileMLE.phitheta | Source code |
| MLE.parallel | Source code |
| PostPhi.NBlogN | Source code |
| Posterior.phi | Source code |
| ShowOnePeak | Man page Source code |
| TRESS_DMRfit | Man page Source code |
| TRESS_DMRtest | Man page Source code |
| TRESS_peak | Man page Source code |
| Uniroot.truncNsd | Source code |
| WaldTest | Source code |
| adjustHessian | Source code |
| d.d2L_R2.phi | Source code |
| d.d2L_R2.theta | Source code |
| d2L.R2 | Source code |
| d2L.Rphi | Source code |
| d2L.Rtheta | Source code |
| d2L.phi2 | Source code |
| d2L.phitheta | Source code |
| d2L.theta2 | Source code |
| d2muj.R2 | Source code |
| dL.R | Source code |
| dL.phi | Source code |
| dL.theta | Source code |
| defineStrand | Source code |
| dmu.R | Source code |
| dmuj.R | Source code |
| exonBins.byTXDB | Source code |
| filterRegions | Man page Source code |
| findBumps | Man page Source code |
| findRegion | Source code |
| getInfer | Source code |
| getLogFC | Source code |
| getPeakCounts | Source code |
| getStrand | Source code |
| getWinCounts | Source code |
| iCovR | Source code |
| iMLE | Source code |
| log.lik_NB | Source code |
| meRatio | Man page Source code |
| mix.2norm.onlysd | Source code |
| mySmooth | Source code |
| mylogit | Source code |
| mysolve | Source code |
| profileMLE.coef | Source code |
| profileMLE.phi | Source code |
| profileMLE.theta | Source code |
| read.BAM | Source code |
