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

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

AuthorXuekui Zhang <xuezhang@jhsph.edu>, Raphael Gottardo <raph@stat.ubc.ca>, Sangsoon Woo <swoo@fhcrc.org>
Date of publicationNone
MaintainerRenan Sauteraud <rsautera@fhcrc.org>
LicenseArtistic-2.0
Version2.18.0

View on Bioconductor

Functions

as.data.frame,pingList-method Man page
bam2gr Man page
chromosome Man page
chromosome,pingError-method Man page
chromosome,pingList-method Man page
chromosome,ping-method Man page
code Man page
code,pingError-method Man page
code,pingList-method Man page
code,ping-method Man page
coerce Man page
coerce,data.frame,pingList-method Man page
coerce,data.frame,pingList-method Man page
coerce,pingList,data.frame-method Man page
coerce,pingList,RangedData-method Man page
CoverageTrack Man page
delta Man page
delta,pingError-method Man page
delta,pingList-method Man page
delta,ping-method Man page
density Man page
density,pingError-method Man page
density,pingList-method Man page
density,ping-method Man page
K Man page
K,pingError-method Man page
K,pingList-method Man page
K,ping-method Man page
length Man page
length,pingList-method Man page
makeRangedDataOutput Man page
maxRange Man page
maxRange,pingError-method Man page
maxRange,pingList-method Man page
maxRange,pingList-method Man page
maxRange,ping-method Man page
minRange Man page
minRange,pingError-method Man page
minRange,pingList-method Man page
minRange,pingList-method Man page
minRange,ping-method Man page
mu Man page
mu,pingError-method Man page
mu,pingList-method Man page
mu,ping-method Man page
newPing Man page
newPingError Man page
newPingError,pingError-method Man page
newPingList Man page
newPingList,pingList-method Man page
newPing,ping-method Man page
NucleosomeTrack Man page
ping Man page
PING Man page
ping-class Man page
pingError Man page
pingError-class Man page
pingList Man page
[,pingList,ANY,ANY-method Man page
[[,pingList,ANY,ANY-method Man page
pingList-class Man page
plot Man page
plot,data.frame,data.frame-method Man page
plot,pingError,segReads-method Man page
plot,pingList,pingList-method Man page
plot,pingList,segReadsList-method Man page
plot,ping,segReads-method Man page
plotSummary Man page
postPING Man page
RawReadsTrack Man page
score Man page
scoreForward Man page
scoreForward,pingError-method Man page
scoreForward,pingList-method Man page
scoreForward,ping-method Man page
score,pingError-method Man page
score,pingList-method Man page
score,ping-method Man page
scoreReverse Man page
scoreReverse,pingError-method Man page
scoreReverse,pingList-method Man page
scoreReverse,ping-method Man page
se Man page
seF Man page
seF,pingError-method Man page
seF,pingList-method Man page
seF,ping-method Man page
segmentPING Man page
segReads Man page
segReadsList Man page
segReadsListPE Man page
segReadsPE Man page
se,pingError-method Man page
se,pingList-method Man page
se,ping-method Man page
seR Man page
seR,pingError-method Man page
seR,pingList-method Man page
seR,ping-method Man page
setParaEM Man page
setParaPrior Man page
show Man page
show-methods Man page
show,pingError-method Man page
show,pingList-method Man page
show,ping-method Man page
show,segReadsList-method Man page
show,segReads-method Man page
sigmaSqF Man page
sigmaSqF,pingError-method Man page
sigmaSqF,pingList-method Man page
sigmaSqF,ping-method Man page
sigmaSqR Man page
sigmaSqR,pingError-method Man page
sigmaSqR,pingList-method Man page
sigmaSqR,ping-method Man page
summary Man page
summary-methods Man page
summary,pingList-method Man page
summary,ping-method Man page
summary,segReadsList-method Man page
summary,segReads-method Man page
w Man page
w,pingError-method Man page
w,pingList-method Man page
w,ping-method Man page

Files

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

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