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.

Files in this package

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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