API for scottzijiezhang/m6Amonster
Analyze m6A seq data
| Global functions | |
|---|---|
| .Bino_test | 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 |
| .fishersMethod | Source code |
| .genoDosage | Source code |
| .get2sides | Source code |
| .getGeneBins | Source code |
| .getGeneModelAnno | 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 |
| Fisher_information | Source code |
| Fisher_information_one_beta | Source code |
| GuitarPlotNew | Man page Source code |
| JointPeakCount | Man page Source code |
| LogLikelihood_beta_psi_mu2 | Source code |
| LogLikelihood_for_individual_sample | Source code |
| LogLikelihood_multiple_beta_psi_mu2 | Source code |
| PoissionGamma | Source code |
| PoissionGamma_FISHER | Source code |
| PoissionGamma_multiple_beta | Source code |
| QNBtest | Man page Source code |
| QTL_PoissonGamma | Man page Source code |
| adjustExprLevel | Man page Source code |
| callPeakBinomial | Source code |
| callPeakFisher | Man page Source code |
| cnetplot.enrichResult | Man page Source code |
| cnetplot_internal | Source code |
| combinedGuitarPlot | Source code |
| coordinate_descent_for_individual_sample | Source code |
| correct_individual_sample | Source code |
| countReads | Man page Source code |
| diffIP | Man page Source code |
| filterPeak | Man page Source code |
| get.col.scale | Source code |
| getAveCoverage | Source code |
| getCov | Source code |
| getTPM | 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 |
| list2graph | Source code |
| log_factorial | Source code |
| log_factorial_calculated | Source code |
| netplot | Source code |
| new_initialization_of_parameters | Source code |
| new_initialization_of_parameters2 | Source code |
| normalizeLibrary | Man page Source code |
| normalizePeak | Man page Source code |
| peakDistribution | Man page Source code |
| plotExpression | Man page Source code |
| plotGene | Man page Source code |
| plotGeneCov | Man page Source code |
| plotGeneCoverage | Man page 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 |
| reportConsistentPeak | Man page Source code |
| reportJointPeak | Man page Source code |
| reportPoissonGammaMerge | Man page Source code |
| scaleNodeColor | Source code |
| 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 |
| setting.graph.attributes | Source code |
