Man pages for scottzijiezhang/MeRIPtools
Analyze MeRIP-seq data and QTL calling
| adjustExprLevel-MeRIP.Peak-method | adjustExprLevel |
| annotatePeak-MeRIP.Peak-method | annotatePeak |
| BetaBinTest | BetaBinTest |
| callPeakBinomial | callPeakBinomial |
| callPeakFisher | callPeakFisher |
| consistentPeak-MeRIP.Peak-method | consistentPeak |
| countReads | countReads |
| counts | counts |
| dot-Bino_test | Binomial test |
| geneBins-MeRIP-method | geneBins |
| geneExpression | extractor for RNAseq data |
| geneExpression-MeRIP.Peak-method | geneExpression |
| geneExpressionTMP | getTPM from geneSum |
| get_peak_logOR | get_peak_logOR |
| gtfToGeneModel | gtfToGeneModel |
| GuitarPlotNew | GuitarPlotNew |
| Input.files | Input.files |
| IP.files | IP.files |
| jointPeakCount | jointPeakCount |
| MetaGene | MetaGene |
| normalizeLibrary-MeRIP.Peak-method | normalizeLibrary |
| peakDistribution | plot distribution of peaks on gene annotation |
| plotGene | old coverage plot function. |
| plotGeneCoverage | plotGeneCoverage |
| plotGeneCov-MeRIP.Peak-method | plotGeneCov |
| plotGeneMonster | plotGeneMonster |
| plotGenePair | plotGenePair |
| plotMetaGene | plotMetaGene |
| plotMetaGeneMulti | plotMEtaGeneMulti A wrapper function for Guitar to plot meta... |
| plotPCAfromMatrix | plotPCAfromMatrix |
| plotTPM | plotTPM |
| PrepCoveragePlot-MeRIP.Peak-method | Prepare coverage plot |
| QNBtest | Wraper function to use QNB package to test for differential... |
| qqplot.pvalue | qqplot.pvalue |
| QTL_BetaBin | QTL_BetaBin |
| QTL_BetaBin2 | QTL_BetaBin2 |
| QTL_BetaBin_permute | QTL_BetaBin_permute |
| QTL_PoissonGamma | QTL_PoissonGamma |
| RADARtest | RADARtest |
| reportJointPeak | reportJointPeak |
| results | export results |
| select | subset MeRIPdata |
| swapChr22.QTL_BetaBin | QTL_BetaBin |
| swapChr22.QTL_BetaBin.permute | swapChr22.QTL_BetaBin.permute |
