Man pages for groHMM
GRO-seq Analysis Pipeline

averagePlotReturns the average profile of tiling array probe intensity...
breakTranscriptsOnGenesbreakTranscriptsOnGenes Breaks transcripts on genes
combineTranscriptscombineTranscripts Combines transnscipts.
countMappableReadsInIntervalcountMappableReadsInInterval counts the number of mappable...
detectTranscriptsdetectTranscripts detects transcripts de novo using a...
evaluateHMMInAnnotationsevaluateHMM Evaluates HMM calling.
expressedGenesFunction identifies expressed features using the methods...
getCoresReturns the number of cores.
getTxDensitygetTxDensity Calculates transcript density.
groHMM-packagegroHMM: GRO-seq Analysis Pipeline
limitToXkblimitToXkb truncates a set of genomic itnervals at a...
makeConsensusAnnotationsmakeConsensusAnnotations Makes a consensus annotation
metaGeneReturns a histogram of the number of reads in each section of...
metaGeneMatrixReturns a matrix, with rows representing read counts across a...
metaGene_nLReturns a histogram of the number of reads in each section of...
pausingIndexReturns the pausing index for different genes. TODO:...
polymeraseWaveGiven GRO-seq data, identifies the location of the polymerase...
readBedreadBed Returns a GenomicRanges object constrcuted from the...
RgammaMLERgammaMLE fits a gamma distribution to a specified data...
RnormRnorm fits a normal distribution to a specified data vector...
Rnorm.expRnorm.exp fits a normal+exponential distribution to a...
runMetaGeneRuns metagene analysis for sense and antisense direction.
tlsDemingA 'total least squares' implementation using demming...
tlsLoessA 'total least squares'-like hack for LOESS. Works by...
tlsSvdA 'total least squares' implementation using singular value...
windowAnalysiswindowAnalysis Returns a vector of integers representing the...
writeWigglewriteWiggle writes a wiggle track or BigWig file suitable for...
groHMM documentation built on May 31, 2017, 11:20 a.m.