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RIPSeeker (version 1.12.0)

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

Description

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.

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Version

Version

1.12.0

License

GPL-2

Maintainer

Yue Li

Last Published

February 15th, 2017

Functions in RIPSeeker (1.12.0)

mainSeekSingleChrom

Automatic bin size selection, bin count, and HMM parameters optimization on read count vector from a single chromosome (Internal function)
nbm_chk

Check the parameters of the negative binomial mixture model
seekRIP

Identify significant peaks
plotStrandedCoverage

Plot strand-specific read coverage for a GRanges object
viewRIP

Visualize peaks from UCSC genome browser.
computeLogOdd

Compute the log odd ratio of RIP over background.
computeRPKM

Compute RPKM based on gene annotations
empiricalFDR

Compute empirical false discovery rate
evalBinSize

Evaluate bin size using Shimazaki cost function
nbh.GRanges

Optimize HMM parameters based on the read counts on a chromosome
binCount

Count reads in nonoverlapping bins across a chromosome
randindx

Generates random indexes with a specified probability distribution
mainSeek

Train HMM paramters on each chromosome independently from the alignments.
addDummyProb

Create a dummy GRanges object as a placeholder in case nbh_em fails (Internal function)
scoreMergedBins

Average log odd scores over bins being merged into a single region
nbh_gen

Simulate data from a negative binomial HMM.
statdis

Returns the stationary distribution of a Markov chain.
annotateRIP

Annotate RIP peaks with genomic information and perform GO enrichement
disambiguateMultihits

Assign each multihit to a unique region based on the posterior for the read-enriched hidden state
logScoreWithoutControl

Compute RIPScore based on RIP posteriors alone and test for significance
nbh.integer

HMM posterior decoding and NB parameter optimization
rulebaseRIPSeek

Compute the RPKM and foldchange between two conditions for the annotated genes
getAlignGal

Import and processs in BAM/SAM/BED format
nbh_chk

Check the parameters of the negative binomial HMM
nbh_vit

Derive maximum likelihood hidden state sequence using Viterbi algorithm
combineRIP

Combined predictions from (presumably) biological replicates.
nbm_em

Expectation conditional maximization of likelihood for negative binomial mixture model
nbh_em

Expectation conditional maximization of negative binomial HMM parameters using forward-backward algorithm
ripSeek

HMM-based de novo RIP predictions using alignment data
selectBinSize

Select optimal bin size based on Shimazaki formula
plotCoverage

Plot read coverage for a GRanges object
nbh_init

Initialize negative binomial HMM parameters using negative binomial mixture model
galp2gal

Convert GAlignmentPairs to GAlignments
logScoreWithControl

Compute RIPScore based on RIP and control posteriors and test for significance
combineAlignGals

Combine alignment files into a single GAlignments object
addPseudoAlignment

Add a psuedoalignment as a placeholder for the chromosome (Internal function)
exportGRanges

Export GRanges object in a specified format
RIPSeeker-package

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

Generic function of negative binomial HMM