API for scottzijiezhang/MeRIPtools
Analyze MeRIP-seq data and QTL calling
| Global functions | |
|---|---|
| .Bino_test | Man page Source code |
| .CountReadsBatch | Source code |
| .combineListOfDataFrame | Source code |
| .combineListOfGRanges | Source code |
| .combineListOfSplicing | Source code |
| .countGuitarDensity | Source code |
| .countReadFromBam | Source code |
| .extractComponent | Source code |
| .fisher_exact_test | Source code |
| .genoDosage | Source code Source code Source code |
| .genotypeDosage | Source code |
| .get2sides | Source code |
| .getGeneModelAnno | Source code |
| .getGenotype | Source code |
| .getNeighborhood | Source code |
| .getPeakBins | Source code |
| .makeFigure_fill | Source code |
| .makeFigure_nofill | Source code |
| .makeGuitarCoordsForSingleIndex | Source code |
| .makeGuitarCoordsFromGRangesList | Source code |
| .makeGuitarCoordsFromTxDb | Source code |
| .multiplot | Source code |
| .noZero | Source code |
| .peakExons | Source code |
| .peakToGRangesList | Source code |
| .spliceSingleTrans | Source code |
| BetaBinTest | Man page |
| Fisher_information | Source code |
| Fisher_information_one_beta | Source code |
| GuitarPlotNew | Man page Source code |
| IP.files | Man page |
| IP.files,MeRIP-method | Man page |
| Input.files | Man page |
| Input.files,MeRIP-method | Man page |
| LogLikelihood_beta_psi_mu2 | Source code |
| LogLikelihood_for_individual_sample | Source code |
| LogLikelihood_multiple_beta_psi_mu2 | Source code |
| MetaGene | Man page Source code |
| PoissionGamma | Source code |
| PoissionGamma_FISHER | Source code |
| PoissionGamma_multiple_beta | Source code |
| PrepCoveragePlot,MeRIP.Peak-method | Man page |
| QNBtest | Man page |
| QTL_BetaBin | Man page Source code |
| QTL_BetaBin2 | Man page |
| QTL_BetaBin_permute | Man page |
| QTL_PoissonGamma | Man page Source code |
| RADARtest | Man page |
| adjustExprLevel,MeRIP.Peak-method | Man page |
| annotatePeak,MeRIP.Peak-method | Man page |
| callPeakBinomial | Man page Source code |
| callPeakFisher | Man page Source code |
| combinedGuitarPlot | Source code |
| consistentPeak,MeRIP.Peak-method | Man page |
| coordinate_descent_for_individual_sample | Source code |
| correct_individual_sample | Source code |
| countReads | Man page Source code |
| countReadsCarRNA | Source code |
| counts,MeRIP-method | Man page |
| counts,MeRIP.Peak-method | Man page |
| extract_gtf_anno | Source code |
| geneBins,MeRIP-method | Man page |
| geneExpression | Man page |
| geneExpression,MeRIP.Peak-method | Man page |
| geneExpressionTMP | Man page |
| getAllCoverage | Source code |
| getAveCoverage | Source code |
| getCov | Source code |
| getTPM | Source code |
| get_peak_logOR | Man page Source code |
| gradient_and_LogLikelihood_for_individual_sample | Source code |
| gradient_beta_psi_mu2 | Source code |
| gradient_descent_alt | Source code |
| gradient_descent_beta_psi_mu2 | Source code |
| gradient_descent_for_individual_sample | Source code |
| gradient_descent_multiple_beta_psi_mu2 | Source code |
| gradient_multiple_beta_psi_mu2 | Source code |
| gtfToGeneModel | Man page Source code |
| jointPeakCount | Man page Source code |
| log_factorial | Source code |
| log_factorial_calculated | Source code |
| makeMeRIPfromList | Source code |
| new_initialization_of_parameters | Source code |
| new_initialization_of_parameters2 | Source code |
| normalizeLibrary,MeRIP.Peak-method | Man page |
| peakDistribution | Man page |
| plotGene | Man page Source code |
| plotGeneCov,MeRIP.Peak-method | Man page |
| plotGeneCoverage | Man page Source code |
| plotGeneCoverageSplit | Source code |
| plotGeneMonster | Man page Source code |
| plotGenePair | Man page Source code |
| plotMetaGene | Man page Source code |
| plotMetaGeneMulti | Man page Source code |
| plotPCA.DESeq2 | Source code |
| plotPCAfromMatrix | Man page Source code |
| plotTPM | Man page Source code |
| qqplot.pvalue | Man page Source code |
| randomPeaks | Source code |
| reportJointPeak | Man page Source code |
| results | Man page |
| select | Man page |
| select_stepsize_for_a_parameter | Source code |
| select_stepsize_for_beta | Source code |
| select_stepsize_for_mu2 | Source code |
| select_stepsize_for_mu2_with_multiple_beta | Source code |
| select_stepsize_for_multiple_beta | Source code |
| select_stepsize_for_psi | Source code |
| select_stepsize_for_psi_with_multiple_beta | Source code |
| swapChr1.QTL_BetaBin | Source code |
| swapChr22.QTL_BetaBin | Man page Source code |
| swapChr22.QTL_BetaBin.permute | Man page |
