Man pages for RIPSeeker
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

addDummyProbCreate a dummy GRanges object as a placeholder in case nbh_em...
addPseudoAlignmentAdd a psuedoalignment as a placeholder for the chromosome...
annotateRIPAnnotate RIP peaks with genomic information and perform GO...
binCountCount reads in nonoverlapping bins across a chromosome
combineAlignGalsCombine alignment files into a single GAlignments object
combineRIPCombined predictions from (presumably) biological replicates.
computeLogOddCompute the log odd ratio of RIP over background.
computeRPKMCompute RPKM based on gene annotations
disambiguateMultihitsAssign each multihit to a unique region based on the...
empiricalFDRCompute empirical false discovery rate
evalBinSizeEvaluate bin size using Shimazaki cost function
exportGRangesExport GRanges object in a specified format
galp2galConvert GAlignmentPairs to GAlignments
getAlignGalImport and processs in BAM/SAM/BED format
logScoreWithControlCompute RIPScore based on RIP and control posteriors and test...
logScoreWithoutControlCompute RIPScore based on RIP posteriors alone and test for...
mainSeekTrain HMM paramters on each chromosome independently from the...
mainSeekSingleChromAutomatic bin size selection, bin count, and HMM parameters...
nbhGeneric function of negative binomial HMM
nbh_chkCheck the parameters of the negative binomial HMM
nbh_emExpectation conditional maximization of negative binomial HMM...
nbh_genSimulate data from a negative binomial HMM.
nbh.GRangesOptimize HMM parameters based on the read counts on a...
nbh_initInitialize negative binomial HMM parameters using negative...
nbh.integerHMM posterior decoding and NB parameter optimization
nbh_vitDerive maximum likelihood hidden state sequence using Viterbi...
nbm_chkCheck the parameters of the negative binomial mixture model
nbm_emExpectation conditional maximization of likelihood for...
plotCoveragePlot read coverage for a GRanges object
plotStrandedCoveragePlot strand-specific read coverage for a GRanges object
randindxGenerates random indexes with a specified probability...
ripSeekHMM-based de novo RIP predictions using alignment data
RIPSeeker-packageRIPSeeker: a statistical package for identifying...
rulebaseRIPSeekCompute the RPKM and foldchange between two conditions for...
scoreMergedBinsAverage log odd scores over bins being merged into a single...
seekRIPIdentify significant peaks
selectBinSizeSelect optimal bin size based on Shimazaki formula
statdisReturns the stationary distribution of a Markov chain.
viewRIPVisualize peaks from UCSC genome browser.
RIPSeeker documentation built on Nov. 17, 2017, 9:08 a.m.