PICS protocols

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description
PICS computational protocol

PICS specifications

Information


Unique identifier OMICS_00455
Name PICS
Alternative name Probabilistic Inference for ChIP-Seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.24.0
Stability Stable
Requirements
methods, stats, parallel, graphics, IRanges, GenomicRanges, Rsamtools, S4Vectors, ShortRead, rtracklayer, R(>=2.14.0), BiocGenerics(>=0.1.3), stats4, grDevices, GenomicAlignments
Maintained Yes

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Documentation


Publication for Probabilistic Inference for ChIP-Seq

PICS IN pipelines

 (2)
2014
PMCID: 4262374
PMID: 25574134
DOI: 10.4137/GRSB.S19711

[…] quality for downstream analysis (supplementary fig. 1, panels a, b). after mapping them on mm9 by cobweb, we identified 56,278 spi1-chip peaks detected by macs and 15,141 spi1-chip peaks detected by pics. from these, we selected peaks located within a distance of 5,000 bp from protein coding genes, and then extracted 5,264 genes overlapping between data derived from two distinct peak-finding […]

2014
PMCID: 4262374
PMID: 25574134
DOI: 10.4137/GRSB.S19711

[…] we selected peaks located within a distance of 5,000 bp from protein coding genes, and then extracted 5,264 genes overlapping between data derived from two distinct peak-finding algorithms macs and pics termed as the most reliable spi1 targets (supplementary table 1). the peaks were accumulated in the upstream (18.7%) and intronic (69.5%) regions. the motif analysis by gadem revealed […]

PICS institution(s)
Department of Statistics, University of British Columbia, Vancouver, BC, Canada; BC Cancer Agency Genome Sciences Centre, Vancouver, BC, Canada; Bioinformatics Training Program, University of British Columbia, Vancouver, BC, Canada; Clinical Research Institute of Montreal (IRCM), Montreal, QC, Canada; Université de Montreal, Montreal, QC, Canada
PICS funding source(s)
Supported by an NSERC Discovery Grant.

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