RIPSeeker: RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.

AuthorYue Li
Date of publicationNone
MaintainerYue Li <yueli@cs.toronto.edu>
LicenseGPL-2
Version1.14.0
http://www.cs.utoronto.ca/~yueli/software.html

View on Bioconductor

Man pages

addDummyProb: Create a dummy GRanges object as a placeholder in case nbh_em...

addPseudoAlignment: Add a psuedoalignment as a placeholder for the chromosome...

annotateRIP: Annotate RIP peaks with genomic information and perform GO...

binCount: Count reads in nonoverlapping bins across a chromosome

combineAlignGals: Combine alignment files into a single GAlignments object

combineRIP: Combined predictions from (presumably) biological replicates.

computeLogOdd: Compute the log odd ratio of RIP over background.

computeRPKM: Compute RPKM based on gene annotations

disambiguateMultihits: Assign each multihit to a unique region based on the...

empiricalFDR: Compute empirical false discovery rate

evalBinSize: Evaluate bin size using Shimazaki cost function

exportGRanges: Export GRanges object in a specified format

galp2gal: Convert GAlignmentPairs to GAlignments

getAlignGal: Import and processs in BAM/SAM/BED format

logScoreWithControl: Compute RIPScore based on RIP and control posteriors and test...

logScoreWithoutControl: Compute RIPScore based on RIP posteriors alone and test for...

mainSeek: Train HMM paramters on each chromosome independently from the...

mainSeekSingleChrom: Automatic bin size selection, bin count, and HMM parameters...

nbh: Generic function of negative binomial HMM

nbh_chk: Check the parameters of the negative binomial HMM

nbh_em: Expectation conditional maximization of negative binomial HMM...

nbh_gen: Simulate data from a negative binomial HMM.

nbh.GRanges: Optimize HMM parameters based on the read counts on a...

nbh_init: Initialize negative binomial HMM parameters using negative...

nbh.integer: HMM posterior decoding and NB parameter optimization

nbh_vit: Derive maximum likelihood hidden state sequence using Viterbi...

nbm_chk: Check the parameters of the negative binomial mixture model

nbm_em: Expectation conditional maximization of likelihood for...

plotCoverage: Plot read coverage for a GRanges object

plotStrandedCoverage: Plot strand-specific read coverage for a GRanges object

randindx: Generates random indexes with a specified probability...

ripSeek: HMM-based de novo RIP predictions using alignment data

RIPSeeker-package: RIPSeeker: a statistical package for identifying...

rulebaseRIPSeek: Compute the RPKM and foldchange between two conditions for...

scoreMergedBins: Average log odd scores over bins being merged into a single...

seekRIP: Identify significant peaks

selectBinSize: Select optimal bin size based on Shimazaki formula

statdis: Returns the stationary distribution of a Markov chain.

viewRIP: Visualize peaks from UCSC genome browser.

Functions

addDummyProb Man page
addPseudoAlignment Man page
annotateRIP Man page
binCount Man page
combineAlignGals Man page
combineRIP Man page
computeLogOdd Man page
computeRPKM Man page
disambiguateMultihits Man page
empiricalFDR Man page
evalBinSize Man page
exportGRanges Man page
galp2gal Man page
getAlignGal Man page
logScoreWithControl Man page
logScoreWithoutControl Man page
mainSeek Man page
mainSeekSingleChrom Man page
nbh Man page
nbh_chk Man page
nbh_em Man page
nbh_gen Man page
nbh.GRanges Man page
nbh_init Man page
nbh.integer Man page
nbh_vit Man page
nbm_chk Man page
nbm_em Man page
plotCoverage Man page
plotStrandedCoverage Man page
randindx Man page
ripSeek Man page
RIPSeeker Man page
RIPSeeker-package Man page
rulebaseRIPSeek Man page
scoreMergedBins Man page
seekRIP Man page
selectBinSize Man page
statdis Man page
viewRIP Man page

Files

RIPSeeker/DESCRIPTION
RIPSeeker/NAMESPACE
RIPSeeker/R
RIPSeeker/R/addDummyProb.R RIPSeeker/R/addPseudoAlignment.R RIPSeeker/R/annotateRIP.R RIPSeeker/R/binCount.R RIPSeeker/R/combineAlignGals.R RIPSeeker/R/combineRIP.R RIPSeeker/R/computeLogOdd.R RIPSeeker/R/computeRPKM.R RIPSeeker/R/disambiguateMultihits.R RIPSeeker/R/empiricalFDR.R RIPSeeker/R/evalBinSize.R RIPSeeker/R/exportGRanges.R RIPSeeker/R/galp2gal.R RIPSeeker/R/getAlignGal.R RIPSeeker/R/logScoreWithControl.R RIPSeeker/R/logScoreWithoutControl.R RIPSeeker/R/mainSeek.R RIPSeeker/R/mainSeekSingleChrom.R RIPSeeker/R/nbh.GRanges.R RIPSeeker/R/nbh.R RIPSeeker/R/nbh.integer.R RIPSeeker/R/nbh_chk.R RIPSeeker/R/nbh_em.R RIPSeeker/R/nbh_gen.R RIPSeeker/R/nbh_init.R RIPSeeker/R/nbh_vit.R RIPSeeker/R/nbm_chk.R RIPSeeker/R/nbm_em.R RIPSeeker/R/plotCoverage.R RIPSeeker/R/randindx.R RIPSeeker/R/ripSeek.R RIPSeeker/R/rulebaseRIPSeek.R RIPSeeker/R/scoreMergedBins.R RIPSeeker/R/seekRIP.R RIPSeeker/R/selectBinSize.R RIPSeeker/R/statdis.R RIPSeeker/R/viewRIP.R
RIPSeeker/build
RIPSeeker/build/vignette.rds
RIPSeeker/inst
RIPSeeker/inst/CITATION
RIPSeeker/inst/NEWS
RIPSeeker/inst/doc
RIPSeeker/inst/doc/RIPSeeker.R
RIPSeeker/inst/doc/RIPSeeker.Rnw
RIPSeeker/inst/doc/RIPSeeker.pdf
RIPSeeker/inst/extdata
RIPSeeker/inst/extdata/PRC2
RIPSeeker/inst/extdata/PRC2/SRR039210_processed_tophat
RIPSeeker/inst/extdata/PRC2/SRR039210_processed_tophat/accepted_hits_noDup_sel_chrX.bam
RIPSeeker/inst/extdata/PRC2/SRR039211_processed_tophat
RIPSeeker/inst/extdata/PRC2/SRR039211_processed_tophat/accepted_hits_noDup_sel_chrX.bam
RIPSeeker/inst/extdata/PRC2/SRR039214_processed_tophat
RIPSeeker/inst/extdata/PRC2/SRR039214_processed_tophat/accepted_hits_noDup_sel_chrX.bam
RIPSeeker/inst/extdata/RIPregions
RIPSeeker/inst/extdata/RIPregions/RIPregion_biorep1.gff3
RIPSeeker/inst/extdata/RIPregions/RIPregion_biorep2.gff3
RIPSeeker/inst/extdata/pairedend
RIPSeeker/inst/extdata/pairedend/ex1.bam
RIPSeeker/man
RIPSeeker/man/RIPSeeker-package.Rd RIPSeeker/man/addDummyProb.Rd RIPSeeker/man/addPseudoAlignment.Rd RIPSeeker/man/annotateRIP.Rd RIPSeeker/man/binCount.Rd RIPSeeker/man/combineAlignGals.Rd RIPSeeker/man/combineRIP.Rd RIPSeeker/man/computeLogOdd.Rd RIPSeeker/man/computeRPKM.Rd RIPSeeker/man/disambiguateMultihits.Rd RIPSeeker/man/empiricalFDR.Rd RIPSeeker/man/evalBinSize.Rd RIPSeeker/man/exportGRanges.Rd RIPSeeker/man/galp2gal.Rd RIPSeeker/man/getAlignGal.Rd RIPSeeker/man/logScoreWithControl.Rd RIPSeeker/man/logScoreWithoutControl.Rd RIPSeeker/man/mainSeek.Rd RIPSeeker/man/mainSeekSingleChrom.Rd RIPSeeker/man/nbh.GRanges.Rd RIPSeeker/man/nbh.Rd RIPSeeker/man/nbh.integer.Rd RIPSeeker/man/nbh_chk.Rd RIPSeeker/man/nbh_em.Rd RIPSeeker/man/nbh_gen.Rd RIPSeeker/man/nbh_init.Rd RIPSeeker/man/nbh_vit.Rd RIPSeeker/man/nbm_chk.Rd RIPSeeker/man/nbm_em.Rd RIPSeeker/man/plotCoverage.Rd RIPSeeker/man/plotStrandedCoverage.Rd RIPSeeker/man/randindx.Rd RIPSeeker/man/ripSeek.Rd RIPSeeker/man/rulebaseRIPSeek.Rd RIPSeeker/man/scoreMergedBins.Rd RIPSeeker/man/seekRIP.Rd RIPSeeker/man/selectBinSize.Rd RIPSeeker/man/statdis.Rd RIPSeeker/man/viewRIP.Rd
RIPSeeker/vignettes
RIPSeeker/vignettes/RIPSeeker.Rnw
RIPSeeker/vignettes/RIPSeeker.bib
RIPSeeker/vignettes/SD.aux
RIPSeeker/vignettes/nar.aux

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