PICS: Probabilistic inference of ChIP-seq

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

Author
Xuekui Zhang <xzhang@stat.ubc.ca>, Raphael Gottardo <rgottard@fhcrc.org>
Date of publication
None
Maintainer
Renan Sauteraud <rsautera@fhcrc.org>
License
Artistic-2.0
Version
2.18.0

View on Bioconductor

Man pages

bam2gr
pre-process bam files
makeRangedDataOutput
Create a RangedData object from a PICS output
PICS
Estimation of binding site positions
pics-class
The pics class
picsError-class
The pics class
picsFDR
Estimate the FDR.
picsList-class
The pics class
plot-FDR
FDR plot for PICS
segChrRead
Segmentation of paired-end sequencing data
segmentPICS
Segment the genome into candidate regions
segReads
Segment the genome into candidate regions
SegReadsList
Segment the genome into candidate regions
segReadsListPE
List of segReadsPE objects
segReadsPE
Class to store post-segmentation result
setParaEM
Function that returns a list of parameters for the EM...
setParaPrior
Function that returns a list of parameters that can be used...
show
show PICS
summary
summary PICS
summarySeg
Summarize a segReadsList object.

Files in this package

PICS/DESCRIPTION
PICS/NAMESPACE
PICS/NEWS
PICS/R
PICS/R/PICS.R
PICS/R/makeRangedDataOutput.R
PICS/R/picsFDR.R
PICS/R/segReadsGeneric.R
PICS/R/segmentPICS.R
PICS/R/segmentReadsPE.R
PICS/R/setClasses.R
PICS/R/setMethods.R
PICS/R/setPara.R
PICS/aclocal.m4
PICS/build
PICS/build/vignette.rds
PICS/cleanup
PICS/configure
PICS/configure.ac
PICS/inst
PICS/inst/CITATION
PICS/inst/doc
PICS/inst/doc/PICS.R
PICS/inst/doc/PICS.Rnw
PICS/inst/doc/PICS.pdf
PICS/inst/extdata
PICS/inst/extdata/Input_tags_chr21_sort.bed
PICS/inst/extdata/Treatment_tags_chr21_sort.bed
PICS/inst/extdata/mapProfileShort
PICS/man
PICS/man/PICS.Rd
PICS/man/SegReadsList.Rd
PICS/man/bam2gr.Rd
PICS/man/makeRangedDataOutput.Rd
PICS/man/pics-class.Rd
PICS/man/picsError-class.Rd
PICS/man/picsFDR.Rd
PICS/man/picsList-class.Rd
PICS/man/plot-FDR.Rd
PICS/man/segChrRead.Rd
PICS/man/segReads.Rd
PICS/man/segReadsListPE.Rd
PICS/man/segReadsPE.Rd
PICS/man/segmentPICS.Rd
PICS/man/setParaEM.Rd
PICS/man/setParaPrior.Rd
PICS/man/show.Rd
PICS/man/summary.Rd
PICS/man/summarySeg.Rd
PICS/src
PICS/src/Makevars.in
PICS/src/Makevars.win
PICS/src/pics.c
PICS/src/segment.c
PICS/vignettes
PICS/vignettes/GPL.txt
PICS/vignettes/PICS.Rnw