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.

Author
Yue Li
Date of publication
None
Maintainer
Yue Li <yueli@cs.toronto.edu>
License
GPL-2
Version
1.14.0
URLs

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