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groHMM (version 1.6.0)

GRO-seq Analysis Pipeline

Description

A pipeline for the analysis of GRO-seq data.

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Version

Version

1.6.0

License

GPL-3

Issues

7

Pull Requests

0

Stars

1

Forks

0

Maintainer

Minho Chae W Lee Kraus leekrausutsouthwesternedu

Last Published

February 15th, 2017

Functions in groHMM (1.6.0)

readBed

readBed Returns a GenomicRanges object constrcuted from the specified bed file.
metaGeneMatrix

Returns a matrix, with rows representing read counts across a specified gene, or other features of interest.
metaGene

Returns a histogram of the number of reads in each section of a moving window centered on a certain feature.
windowAnalysis

windowAnalysis Returns a vector of integers representing the counts of reads in a moving window.
Rnorm

Rnorm fits a normal distribution to a specified data vector using maximum likelihood.
groHMM-package

groHMM: GRO-seq Analysis Pipeline
tlsDeming

A 'total least squares' implementation using demming regression.
detectTranscripts

detectTranscripts detects transcripts de novo using a two-state hidden Markov model (HMM).
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').
expressedGenes

Function identifies expressed features using the methods introduced in Core, Waterfall, Lis; Science, Dec. 2008.
getTxDensity

getTxDensity Calculates transcript density.
RgammaMLE

RgammaMLE fits a gamma distribution to a specified data vector using maximum likelihood.
runMetaGene

Runs metagene analysis for sense and antisense direction.
breakTranscriptsOnGenes

breakTranscriptsOnGenes Breaks transcripts on genes
evaluateHMMInAnnotations

evaluateHMM Evaluates HMM calling.
makeConsensusAnnotations

makeConsensusAnnotations Makes a consensus annotation
metaGene_nL

Returns a histogram of the number of reads in each section of a moving window of #' variable size across genes.
writeWiggle

writeWiggle writes a wiggle track or BigWig file suitable for uploading to the UCSC genome browser.
polymeraseWave

Given GRO-seq data, identifies the location of the polymerase 'wave' in up- or down- regulated genes.
combineTranscripts

combineTranscripts Combines transnscipts.
countMappableReadsInInterval

countMappableReadsInInterval counts the number of mappable reads in a set of genomic features.
Rnorm.exp

Rnorm.exp fits a normal+exponential distribution to a specified data vector using maximum likelihood.
tlsLoess

A 'total least squares'-like hack for LOESS. Works by rotating points 45 degrees, fitting LOESS, and rotating back.
tlsSvd

A 'total least squares' implementation using singular value demposition.
getCores

Returns the number of cores.
pausingIndex

Returns the pausing index for different genes. TODO: DESCRIBE THE PAUSING INDEX.
limitToXkb

limitToXkb truncates a set of genomic itnervals at a constant, maximum size.