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groHMM (version 1.4.0)
GRO-seq Analysis Pipeline.
Description
A pipeline for the analysis of GRO-seq data.
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Version
1.4.0
License
GPL-3
Maintainer
Minho Chae W Lee Kraus leekrausutsouthwesternedu
Last Published
July 20th, 2015
Functions in groHMM (1.4.0)
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getTxDensity
getTxDensity Calculates transcript density.
RgammaMLE
RgammaMLE fits a gamma distribution to a specified data vector using maximum likelihood.
Rnorm.exp
Rnorm.exp fits a normal+exponential distribution to a specified data vector using maximum likelihood.
groHMM-package
groHMM: GRO-seq Analysis Pipeline
averagePlot
Returns the average profile of tiling array probe intensity values or wiggle-like count data centered on a set of genomic positions (specified by 'Peaks').
breakTranscriptsOnGenes
breakTranscriptsOnGenes Breaks transcripts on genes
metaGene_nL
Returns a histogram of the number of reads in each section of a moving window of #' variable size across genes.
metaGene
Returns a histogram of the number of reads in each section of a moving window centered on a certain feature.
getCores
Returns the number of cores.
expressedGenes
Function identifies expressed features using the methods introduced in Core, Waterfall, Lis; Science, Dec. 2008.
limitToXkb
limitToXkb truncates a set of genomic itnervals at a constant, maximum size.
writeWiggle
writeWiggle writes a wiggle track or BigWig file suitable for uploading to the UCSC genome browser.
makeConsensusAnnotations
makeConsensusAnnotations Makes a consensus annotation
Rnorm
Rnorm fits a normal distribution to a specified data vector using maximum likelihood.
runMetaGene
Runs metagene analysis for sense and antisense direction.
metaGeneMatrix
Returns a matrix, with rows representing read counts across a specified gene, or other features of interest.
pausingIndex
Returns the pausing index for different genes. TODO: DESCRIBE THE PAUSING INDEX.
tlsDeming
A 'total least squares' implementation using demming regression.
tlsLoess
A 'total least squares'-like hack for LOESS. Works by rotating points 45 degrees, fitting LOESS, and rotating back.
combineTranscripts
combineTranscripts Combines transnscipts.
countMappableReadsInInterval
countMappableReadsInInterval counts the number of mappable reads in a set of genomic features.
readBed
readBed Returns a GenomicRanges object constrcuted from the specified bed file.
polymeraseWave
Given GRO-seq data, identifies the location of the polymerase 'wave' in up- or down- regulated genes.
detectTranscripts
detectTranscripts detects transcripts de novo using a two-state hidden Markov model (HMM).
evaluateHMMInAnnotations
evaluateHMM Evaluates HMM calling.
tlsSvd
A 'total least squares' implementation using singular value demposition.
windowAnalysis
windowAnalysis Returns a vector of integers representing the counts of reads in a moving window.