API for scottzijiezhang/MeRIPtools
Analyze MeRIP-seq data and QTL calling

Global functions
.Bino_test Man page 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
.getGeneBins 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
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
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
scottzijiezhang/MeRIPtools documentation built on Nov. 5, 2019, 8:46 a.m.