groHMM: GRO-seq Analysis Pipeline

A pipeline for the analysis of GRO-seq data.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("groHMM")
AuthorCharles G. Danko, Minho Chae, Andre Martins, W. Lee Kraus
Bioconductor views Sequencing Software
Date of publicationNone
MaintainerAnusha Nagari <anusha.nagari@utsouthwestern.edu>, Venkat Malladi <venkat.malladi@utsouthwestern.edu>, Tulip Nandu <tulip.nandu@utsouthwestern.edu>, W. Lee Kraus <lee.kraus@utsouthwestern.edu>
LicenseGPL-3
Version1.10.0
https://github.com/Kraus-Lab/groHMM

View on Bioconductor

Man pages

averagePlot: Returns the average profile of tiling array probe intensity...

breakTranscriptsOnGenes: breakTranscriptsOnGenes Breaks transcripts on genes

combineTranscripts: combineTranscripts Combines transnscipts.

countMappableReadsInInterval: countMappableReadsInInterval counts the number of mappable...

detectTranscripts: detectTranscripts detects transcripts de novo using a...

evaluateHMMInAnnotations: evaluateHMM Evaluates HMM calling.

expressedGenes: Function identifies expressed features using the methods...

getCores: Returns the number of cores.

getTxDensity: getTxDensity Calculates transcript density.

groHMM-package: groHMM: GRO-seq Analysis Pipeline

limitToXkb: limitToXkb truncates a set of genomic itnervals at a...

makeConsensusAnnotations: makeConsensusAnnotations Makes a consensus annotation

metaGene: Returns a histogram of the number of reads in each section of...

metaGeneMatrix: Returns a matrix, with rows representing read counts across a...

metaGene_nL: Returns a histogram of the number of reads in each section of...

pausingIndex: Returns the pausing index for different genes. TODO:...

polymeraseWave: Given GRO-seq data, identifies the location of the polymerase...

readBed: readBed Returns a GenomicRanges object constrcuted from the...

RgammaMLE: RgammaMLE fits a gamma distribution to a specified data...

Rnorm: Rnorm fits a normal distribution to a specified data vector...

Rnorm.exp: Rnorm.exp fits a normal+exponential distribution to a...

runMetaGene: Runs metagene analysis for sense and antisense direction.

tlsDeming: A 'total least squares' implementation using demming...

tlsLoess: A 'total least squares'-like hack for LOESS. Works by...

tlsSvd: A 'total least squares' implementation using singular value...

windowAnalysis: windowAnalysis Returns a vector of integers representing the...

writeWiggle: writeWiggle writes a wiggle track or BigWig file suitable for...

Functions

averagePlot Man page
breakTranscriptsOnGenes Man page
combineTranscripts Man page
countMappableReadsInInterval Man page
detectTranscripts Man page
evaluateHMMInAnnotations Man page
expressedGenes Man page
getCores Man page
getTxDensity Man page
groHMM Man page
groHMM-package Man page
limitToXkb Man page
makeConsensusAnnotations Man page
metaGene Man page
metaGeneMatrix Man page
metaGene_nL Man page
pausingIndex Man page
polymeraseWave Man page
readBed Man page
RgammaMLE Man page
Rnorm Man page
Rnorm.exp Man page
runMetaGene Man page
tlsDeming Man page
tlsLoess Man page
tlsSvd Man page
windowAnalysis Man page
writeWiggle Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.