enRich: An R Package for the Analysis of Multiple ChIP-Seq Data
Version 3.0

An R package for joint statistical modelling of ChIP-seq data, accounting for technical/biological replicates, multiple conditions and different ChIP efficiencies of the individual experiments.

AuthorYanchun Bao, Veronica Vinciotti
Date of publication2015-10-24 18:19:26
MaintainerYanchun Bao <ybaoa@essex.ac.uk>
LicenseGPL-2
Version3.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("enRich")

Getting started

Package overview

Popular man pages

enrich.mix: Detection of enriched and differentially bound regions for...
enRich-package: An R package for the analysis of multiple ChIP-seq data.
FDR: Identification of enriched regions by controlling a given FDR...
IPE: Estimating the ImmunoPrecipitation (IP) efficiency of a...
mrf.joint: Joint fitting of a one-dimensional Markov random field model...
p300cbp.1000bp: Example Data
p300cbp.200bp: Example Data
See all...

All man pages Function index File listing

Man pages

enrich.mix: Detection of enriched and differentially bound regions for...
enrich.mrf: Detection of enriched and differentially bound regions for...
enRich-package: An R package for the analysis of multiple ChIP-seq data.
FDR: Identification of enriched regions by controlling a given FDR...
IPE: Estimating the ImmunoPrecipitation (IP) efficiency of a...
mix: Fitting mixture of two densities, either Poisson or Negative...
mix.joint: Joint fitting of mixture of Poisson or NB densities to...
mrf: Fitting a one-dimensional Markov random field mixture model...
mrf.joint: Joint fitting of a one-dimensional Markov random field model...
p300cbp.1000bp: Example Data
p300cbp.200bp: Example Data

Functions

FDR Man page Source code
IPE Man page Source code
NBlike_phi_offset Source code
enRich Man page
enRich-package Man page
enrich.mix Man page Source code
enrich.mrf Man page Source code
mix Man page Source code
mix.joint Man page Source code
mix_offset Source code Source code
mix_single Source code
mix_srsp1 Source code
mloglike_offsetNB Source code
mloglike_offsetpois Source code
mrf Man page Source code
mrf.joint Man page Source code
mrf_rep Source code
mrf_single Source code
mrf_sp Source code
mrf_srsp Source code
p300cbp.1000bp Man page
p300cbp.200bp Man page
pprob Source code
pprob_joint Source code

Files

src
src/MRF.c
src/MRFsrsp.c
src/MRFrep.c
src/MRFsp.c
NAMESPACE
data
data/p300cbp.200bp.rda
data/datalist
data/p300cbp.1000bp.rda
R
R/pprob.R
R/IPE.R
R/pprob_joint.R
R/enrich.mix.R
R/mixfit_offset.R
R/mrf_sp.R
R/mloglike_offsetNB.R
R/mix_single.R
R/NBlike_phi_offset.R
R/FDR.R
R/mrf_srsp.R
R/mix.R
R/mix.joint.R
R/mix_srsp1.R
R/mrf.joint.R
R/mix_offset.R
R/mloglike_offsetpois.R
R/mrf_single.R
R/enrich.mrf.R
R/mrf_rep.R
R/mrf.R
MD5
DESCRIPTION
man
man/mrf.Rd
man/mix.joint.Rd
man/mix.Rd
man/FDR.Rd
man/IPE.Rd
man/enrich.mrf.Rd
man/p300cbp.200bp.Rd
man/p300cbp.1000bp.Rd
man/enRich-package.Rd
man/mrf.joint.Rd
man/enrich.mix.Rd
enRich documentation built on May 20, 2017, 12:17 a.m.

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