PING: Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data

Share:

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

Author
Xuekui Zhang <xuezhang@jhsph.edu>, Raphael Gottardo <raph@stat.ubc.ca>, Sangsoon Woo <swoo@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

CoverageTrack
Reads coverage track
NucleosomeTrack
Track for the Nucleosome position
PICS_IMPORT
PICS functions.
PING
Estimation of binding site positions
ping-class
The ping class
pingError-class
The ping class
pingList-class
The ping class
plotSummary
Plot a summary of the prediction for given ranges.
postPING
Post process Estimation of binding site positions obtained...
RawReadsTrack
Raw reads density track
segmentPING
Segment the genome into candidate regions
show
show PING
summary
summary PING

Files in this package

PING/DESCRIPTION
PING/NAMESPACE
PING/R
PING/R/PING.R
PING/R/postPING.R
PING/R/segmentPING.R
PING/R/setClasses.R
PING/R/setMethods.R
PING/aclocal.m4
PING/build
PING/build/vignette.rds
PING/cleanup
PING/configure
PING/configure.ac
PING/inst
PING/inst/CITATION
PING/inst/NEWS
PING/inst/doc
PING/inst/doc/PING-PE.R
PING/inst/doc/PING-PE.Rnw
PING/inst/doc/PING-PE.pdf
PING/inst/doc/PING.R
PING/inst/doc/PING.Rnw
PING/inst/doc/PING.pdf
PING/inst/extdata
PING/inst/extdata/GSM351492_R4_chr1.bed
PING/inst/extdata/yeastChrI.bam
PING/man
PING/man/CoverageTrack.Rd
PING/man/NucleosomeTrack.Rd
PING/man/PICS_IMPORT.Rd
PING/man/PING.Rd
PING/man/RawReadsTrack.Rd
PING/man/ping-class.Rd
PING/man/pingError-class.Rd
PING/man/pingList-class.Rd
PING/man/plotSummary.Rd
PING/man/postPING.Rd
PING/man/segmentPING.Rd
PING/man/show.Rd
PING/man/summary.Rd
PING/src
PING/src/Makevars.in
PING/src/Makevars.win
PING/src/init.c
PING/src/ping.c
PING/src/ping.h
PING/vignettes
PING/vignettes/GPL.txt
PING/vignettes/PING-PE.Rnw
PING/vignettes/PING.Rnw