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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 pipeline

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

[…] an acceptable quality for downstream analysis (, 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 […]


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PICS in publications

 (4)
PMCID: 5114576
PMID: 27841260
DOI: 10.1038/ncomms13471

[…] aggregate gene plot was shown by ngs.plot using the mapped reads in which the reads from three biological replicates were pooled., the peaks were called by comparing chip dna with input dna, using pics and erd algorithms on strand ngs software (agilent technologies, palo alto, ca, usa). the overlapping regions of two criteria were determined as peaks. the pics and erd were run using a default […]

PMCID: 4962548
PMID: 27468311
DOI: 10.1186/s13072-016-0082-4

[…] affinity-purified gaf antibody, followed by deep sequencing (chip-seq) to get more than thirty million reads (~32 × 106 for gaf, ~34 × 106 for input), which were used for further analyses. using the pics program (probabilistic inference for chip-seq) [], we identified 3716 gaf binding peaks (fdr < 0.05). subsequent analysis by the meme (multiple em for motif elicitation) program revealed […]

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

[…] (bowtie-bio.sourceforge.net/bowtie2/index.shtml). then, we identified the peaks of binding sites with fold enrichment (fe) ≥5 by using the model-based analysis of chip-seq (macs) program or the probabilistic inference for chip-seq (pics) program., we determined the genes corresponding to the peaks by a neighboring gene analysis tool of strand ngs in the setting within a distance of 5,000 bp […]

PMCID: 3136941
PMID: 21779396
DOI: 10.1371/journal.pone.0022226

[…] procedures with mbd-seq. these programs apply similar or more advanced algorithms compared to the existing mbd-seq analysis methods most of which are based on tags density. macs, quest, sissrs and pics were chosen because each of these programs is implemented with different algorithms and uses different statistical methods. for example, the macs algorithm is based on shifting sequence tags […]


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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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