PICS: Probabilistic inference of ChIP-seq

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

AuthorXuekui Zhang <xzhang@stat.ubc.ca>, Raphael Gottardo <rgottard@fhcrc.org>
Date of publicationNone
MaintainerRenan Sauteraud <rsautera@fhcrc.org>
LicenseArtistic-2.0
Version2.18.0

View on Bioconductor

Functions

as.list,AlignedRead-method Man page
bam2gr Man page
candidate.region Man page
chromosome Man page
chromosome,data.frame-method Man page
chromosome,picsError-method Man page
chromosome,picsList-method Man page
chromosome,pics-method Man page
code Man page
code,picsError-method Man page
code,picsList-method Man page
code,pics-method Man page
coerce Man page
coerce,AlignedRead,GenomeData-method Man page
coerce,data.frame,GenomeData-method Man page
coerce,data.frame,GRanges-method Man page
coerce,data.frame,picsList-method Man page
coerce,data.frame,picsList-method Man page
coerce,picsList,data.frame-method Man page
coerce,picsList,RangedData-method Man page
coerce,RangedData,GenomeData-method Man page
delta Man page
delta,data.frame-method Man page
delta,picsError-method Man page
delta,picsList-method Man page
delta,pics-method Man page
density,picsList-method Man page
FDR Man page
\%in\%,ANY,segReads-method Man page
K Man page
K,picsError-method Man page
K,picsList-method Man page
K,pics-method Man page
length Man page
length,picsList-method Man page
length,segReadsList-method Man page
makeRangedDataOutput Man page
map Man page
map,segReadsList-method Man page
map,segReads-method Man page
maxRange Man page
maxRange,picsError-method Man page
maxRange,picsList-method Man page
maxRange,picsList-method Man page
maxRange,pics-method Man page
minRange Man page
minRange,picsError-method Man page
minRange,picsList-method Man page
minRange,picsList-method Man page
minRange,pics-method Man page
mu Man page
mu,data.frame-method Man page
mu,picsError-method Man page
mu,picsList-method Man page
mu,pics-method Man page
newPics Man page
newPicsError Man page
newPicsError,picsError-method Man page
newPicsList Man page
newPicsList,picsList-method Man page
newPics,pics-method Man page
pics Man page
PICS Man page
pics-class Man page
picsError Man page
picsError-class Man page
picsFDR Man page
picsList Man page
[,picsList,ANY,ANY-method Man page
[[,picsList,ANY,ANY-method Man page
picsList-class Man page
[,picsList-method Man page
[[,picsList-method Man page
plot,picsError,segReads-method Man page
plot,picsList,picsList-method Man page
plot,picsList,segReadsList-method Man page
plot,pics,segReads-method Man page
score Man page
score,data.frame-method Man page
scoreForward Man page
scoreForward,data.frame-method Man page
scoreForward,picsError-method Man page
scoreForward,picsList-method Man page
scoreForward,pics-method Man page
score,picsError-method Man page
score,picsList-method Man page
score,pics-method Man page
scoreReverse Man page
scoreReverse,data.frame-method Man page
scoreReverse,picsError-method Man page
scoreReverse,picsList-method Man page
scoreReverse,pics-method Man page
se Man page
se,data.frame-method Man page
seF Man page
seF,data.frame-method Man page
seF,picsError-method Man page
seF,picsList-method Man page
seF,pics-method Man page
segChrRead Man page
segmentPICS Man page
segReads Man page
segReads-class Man page
segReadsGeneric Man page
segReadsList Man page
[,segReadsList,ANY,ANY-method Man page
[[,segReadsList,ANY,ANY-method Man page
segReadsList-class Man page
[,segReadsList-method Man page
[[,segReadsList-method Man page
segReadsListPE Man page
[,segReadsListPE,ANY,ANY-method Man page
[[,segReadsListPE,ANY,ANY-method Man page
segReadsListPE-class Man page
[,segReadsListPE-method Man page
segReadsPE Man page
segReadsPE-class Man page
se,picsError-method Man page
se,picsList-method Man page
se,pics-method Man page
seR Man page
seR,data.frame-method Man page
seR,picsError-method Man page
seR,picsList-method Man page
seR,pics-method Man page
setParaEM Man page
setParaPrior Man page
show Man page
show-methods Man page
show,picsError-method Man page
show,picsList-method Man page
show,pics-method Man page
show,segReadsList-method Man page
show,segReads-method Man page
sigmaSqF Man page
sigmaSqF,data.frame-method Man page
sigmaSqF,picsError-method Man page
sigmaSqF,picsList-method Man page
sigmaSqF,pics-method Man page
sigmaSqR Man page
sigmaSqR,data.frame-method Man page
sigmaSqR,picsError-method Man page
sigmaSqR,picsList-method Man page
sigmaSqR,pics-method Man page
summary Man page
summary-methods Man page
summary,picsList-method Man page
summary,pics-method Man page
summarySeg Man page
summary,segReadsList-method Man page
summary,segReads-method Man page
w Man page
w,data.frame-method Man page
wigDensity Man page
wigDensity,picsError-method Man page
wigDensity,picsList-method Man page
wigDensity,pics-method Man page
w,picsError-method Man page
w,picsList-method Man page
w,pics-method Man page

Files

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

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