groHMM: GRO-seq Analysis Pipeline

A pipeline for the analysis of GRO-seq data.

AuthorCharles G. Danko, Minho Chae, Andre Martins, W. Lee Kraus
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
Version1.8.0
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...

Files in this package

groHMM/DESCRIPTION
groHMM/NAMESPACE
groHMM/R
groHMM/R/breakTranscriptsOnGenes.R groHMM/R/detectTranscripts.R groHMM/R/expressedGenes.R groHMM/R/fitDistributions.R groHMM/R/getTxDensity.R groHMM/R/limitToXkb.R groHMM/R/makeConsensusAnnotations.R groHMM/R/metaGene.R groHMM/R/pausingIndex.R groHMM/R/polymeraseWave.R groHMM/R/tlsFits.R groHMM/R/windowAnalysis.R groHMM/R/writeWiggle.R groHMM/R/zzz.R
groHMM/build
groHMM/build/vignette.rds
groHMM/inst
groHMM/inst/CITATION
groHMM/inst/NEWS
groHMM/inst/doc
groHMM/inst/doc/groHMM.R
groHMM/inst/doc/groHMM.Rnw
groHMM/inst/doc/groHMM.pdf
groHMM/inst/extdata
groHMM/inst/extdata/S0mR1.bam
groHMM/inst/extdata/S40mR1.bam
groHMM/inst/extdata/Vignette.RData
groHMM/man
groHMM/man/RgammaMLE.Rd groHMM/man/Rnorm.Rd groHMM/man/Rnorm.exp.Rd groHMM/man/averagePlot.Rd groHMM/man/breakTranscriptsOnGenes.Rd groHMM/man/combineTranscripts.Rd groHMM/man/countMappableReadsInInterval.Rd groHMM/man/detectTranscripts.Rd groHMM/man/evaluateHMMInAnnotations.Rd groHMM/man/expressedGenes.Rd groHMM/man/getCores.Rd groHMM/man/getTxDensity.Rd groHMM/man/groHMM-package.Rd groHMM/man/limitToXkb.Rd groHMM/man/makeConsensusAnnotations.Rd groHMM/man/metaGene.Rd groHMM/man/metaGeneMatrix.Rd groHMM/man/metaGene_nL.Rd groHMM/man/pausingIndex.Rd groHMM/man/polymeraseWave.Rd groHMM/man/readBed.Rd groHMM/man/runMetaGene.Rd groHMM/man/tlsDeming.Rd groHMM/man/tlsLoess.Rd groHMM/man/tlsSvd.Rd groHMM/man/windowAnalysis.Rd groHMM/man/writeWiggle.Rd
groHMM/src
groHMM/src/AnnotateProbes.c
groHMM/src/DecayAlgorithm.c
groHMM/src/MLEfit.c
groHMM/src/RegisterRRoutines.c
groHMM/src/UsefulValues.h
groHMM/src/Windowing.c
groHMM/src/hmmEM.c
groHMM/src/hmmFwBw.c
groHMM/src/hmmHeader.h
groHMM/src/hmmMiscFunctions.c
groHMM/src/hmmViterbi.c
groHMM/vignettes
groHMM/vignettes/GROseqData.png
groHMM/vignettes/GROseqHMM.png
groHMM/vignettes/groHMM.Rnw
groHMM/vignettes/groHMM.bib

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

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