Package: groHMM 1.41.0

Tulip Nandu

groHMM: GRO-seq Analysis Pipeline

A pipeline for the analysis of GRO-seq data.

Authors:Charles G. Danko, Minho Chae, Andre Martins, W. Lee Kraus

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groHMM.pdf |groHMM.html✨
groHMM/json (API)
NEWS

# Install 'groHMM' in R:
install.packages('groHMM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kraus-lab/grohmm/issues

On BioConductor:groHMM-1.41.0(bioc 3.21)groHMM-1.39.0(bioc 3.20)

sequencingsoftware

5.18 score 1 stars 25 scripts 328 downloads 6 mentions 26 exports 51 dependencies

Last updated 15 days agofrom:8d0b05adb8. Checks:OK: 1 WARNING: 5 NOTE: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 06 2024
R-4.5-win-x86_64WARNINGOct 31 2024
R-4.5-linux-x86_64WARNINGOct 31 2024
R-4.4-win-x86_64WARNINGDec 06 2024
R-4.4-mac-x86_64WARNINGDec 06 2024
R-4.4-mac-aarch64WARNINGDec 06 2024
R-4.3-win-x86_64NOTEDec 06 2024
R-4.3-mac-x86_64NOTEDec 06 2024
R-4.3-mac-aarch64NOTEDec 06 2024

Exports:averagePlotbreakTranscriptsOnGenescombineTranscriptscountMappableReadsInIntervaldetectTranscriptsevaluateHMMInAnnotationsexpressedGenesgetCoresgetTxDensitylimitToXkbmakeConsensusAnnotationsmetaGenemetaGene_nLmetaGeneMatrixpausingIndexpolymeraseWavereadBedRgammaMLERnormRnorm.exprunMetaGenetlsDemingtlsLoesstlsSvdwindowAnalysiswriteWiggle

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMASSMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc

groHMM tutorial

Rendered fromgroHMM.Rnwusingutils::Sweaveon Dec 06 2024.

Last update: 2024-12-03
Started: 2017-10-19

Readme and manuals

Help Manual

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