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RIPSeeker specifications

Information


Unique identifier OMICS_00569
Name RIPSeeker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM, BAM, BED
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.20.0
Stability Stable
Requirements
methods, parallel, IRanges, GenomicRanges, Rsamtools, rtracklayer, GenomicAlignments, SummarizedExperiment, R(>=2.15), S4Vectors(>=0.9.25), biomaRt, ChIPpeakAnno, GenomicFeatures
Maintained Yes

Subtool


  • ripSeek

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Documentation


Publication for RIPSeeker

RIPSeeker in publications

 (5)
PMCID: 5492891
PMID: 28662698
DOI: 10.1186/s12915-017-0387-1

[…] rnas bound to mov10. the total number of reads was 98,884,367; the number of aligned reads was 71,522,027 (74.59% aligned), and the number of uniquely aligned reads was 57,005,129 (59.45%). we used ripseeker to identify rnas significantly enriched over input rna [] and found 2996 rip peaks: 1313 overlapped with repeat elements from the long terminal repeat (ltr) family, the autonomous non-ltr […]

PMCID: 5323403
PMID: 28286470
DOI: 10.3389/fnmol.2017.00045

[…] () packages. for a detailed step-by-step guide to using both of these packages see (). both deseq2 and edger can be used for dge analysis of rip-seq data. however, an alternative package called ripseeker has been developed recently that uses peak-calling, a strategy employed in chip-seq/clip-seq data analysis, and boasts better modeling accuracy than deseq2 and edger for rip-seq data (). […]

PMCID: 5333057
PMID: 28208661
DOI: 10.3390/genes8020068

[…] genome_bowtie.fa -l c2,c4,c6,c7 -u annotation.gtf ./tophat_output_c2/accepted_hits.bam ./tophat_output_c4/accepted_hits.bam ./tophat_output_c6/accepted_hits.bam ./tophat_output_c7/accepted_hits.bam, ripseeker is an r package that was designed specifically to detect significantly enriched peaks in rip-seq data []. bin size was first optimized per chromosome by testing bins ranging from 200 to 400 […]

PMCID: 4498740
PMID: 26162078
DOI: 10.1371/journal.pone.0129321

[…] q-values., pre-processing and read summarization of rip-seq data was carried out as described for the rna-seq data. for each animal (n = 3), a hur and igg1 sample was processed separately using the ripseeker [] algorithm, which is a de novo method for detecting peaks (indicating protein–rna interactions) based on hidden markov models (hmm). this is carried out in a multistage process whereby […]

PMCID: 4719072
PMID: 26041786
DOI: 10.1093/bib/bbv031

[…] number of cims or par-clip transitions in each cluster reduced the number of false hits. a number of sophisticated algorithms have been developed, e.g. paralyzer [], piranha [], wavcluster [], ripseeker [], miclip [], pipe-clip [] and the pyicoclip module of the pyicoteo toolkit (previously called pyicos) []. while different in implementation, all these procedures can be summarized […]


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RIPSeeker institution(s)
Department of Computer Science, University of Toronto, Toronto, ON, Canada; The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
RIPSeeker funding source(s)
Ontario Research Fund - Global Leader (Round 2); Natural Sciences and Engineering Research Council (NSERC) [327612]; NSERC Canada Graduate Scholarship and Ontario Graduate Scholarship

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