groHMM: GRO-seq Analysis Pipeline

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A pipeline for the analysis of GRO-seq data.

Author
Charles G. Danko, Minho Chae, Andre Martins, W. Lee Kraus
Date of publication
None
Maintainer
Anusha Nagari <anusha.nagari@utsouthwestern.edu>, Venkat Malladi <venkat.malladi@utsouthwestern.edu>, Tulip Nandu <tulip.nandu@utsouthwestern.edu>, W. Lee Kraus <lee.kraus@utsouthwestern.edu>
License
GPL-3
Version
1.8.0
URLs

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