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PICS (version 2.16.0)

Probabilistic inference of ChIP-seq

Description

Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.

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Version

Version

2.16.0

License

Artistic-2.0

Maintainer

Renan Sauteraud

Last Published

February 15th, 2017

Functions in PICS (2.16.0)

segReadsListPE

List of segReadsPE objects
picsError-class

The pics class
segmentPICS

Segment the genome into candidate regions
picsFDR

Estimate the FDR.
plot-FDR

FDR plot for PICS
bam2gr

pre-process bam files
summary

summary PICS
setParaPrior

Function that returns a list of parameters that can be used as an argument of PICS.
setParaEM

Function that returns a list of parameters for the EM algorithm that can be used as an argument of PICS.
show

show PICS
segReads

Segment the genome into candidate regions
pics-class

The pics class
segChrRead

Segmentation of paired-end sequencing data
segReadsList

Segment the genome into candidate regions
picsList-class

The pics class
pics

Estimation of binding site positions
makeRangedDataOutput

Create a RangedData object from a PICS output
segReadsPE

Class to store post-segmentation result
summarySeg

Summarize a segReadsList object.