RIPSeeker infers and discriminates 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. In addition, a rule-based approach is provided as an additional function named rulebaseRIPSeek for user to obtain RPKM/FPKM (and fold-change) for the gene/transcripts expressions in RIP (and control) based on automatically retrieved online Ensembl annotation given single or paired-end alignments.
● Data Source:
BioConductor
● Keywords:
● Alias: RIPSeeker, RIPSeeker-package
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This function is used to generate a place holder in cases the EM fails to converge on a chromosome due to too few number of reads mapped to that chromosome. This is an internal function not expected to be directly called by the user.
● Data Source:
BioConductor
● Keywords:
● Alias: addDummyProb
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Check whether chromosome has at least one alignment to prevent abnormal behaviour of the subsequent functions. In case no alignment is found on an entire chromosome, add a pseudo-alignment as a placeholder for that chromosome.
● Data Source:
BioConductor
● Keywords:
● Alias: addPseudoAlignment
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Given the genomic coordinates of each predicted RIP regions, query the Ensembl database whether each region is nearby or overlaps any known (noncoding) genes.
● Data Source:
BioConductor
● Keywords:
● Alias: annotateRIP
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Stratify chromosome into nonoverlapping bins of the same size and count the number of reads that fall within each bin.
● Data Source:
BioConductor
● Keywords:
● Alias: binCount
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Import and process individual BAM/SAM/BED alignment files using getAlignGal and combine them into a single GAlignments.
● Data Source:
BioConductor
● Keywords:
● Alias: combineAlignGals
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A simple helper function that combines multiple prediction lists from biological replicates into a single list.
● Data Source:
BioConductor
● Keywords:
● Alias: combineRIP
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The RIPScore is computed as the log odd ratio of the posterior for the RIP state (z_i = 2) over the posterior for the background state (z_i = 1)
● Data Source:
BioConductor
● Keywords:
● Alias: computeLogOdd
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Given a list of single-end or paired-end read alignment files in BAM/SAM/BED format, compute the read counts and normalized read counts as expression of annotated transcript in the unit of "reads per kilobase of exon per million mapped reads" (RPKM).
● Data Source:
BioConductor
● Keywords:
● Alias: computeRPKM
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Among multiple alignments of the same read (i.e. multihit), select the alignment corresponding to the bin with the maximum posterior for the enriched state.
● Data Source:
BioConductor
● Keywords:
● Alias: disambiguateMultihits
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