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

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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.

Author
Yanchun Bao, Veronica Vinciotti
Date of publication
2015-10-24 18:19:26
Maintainer
Yanchun Bao <ybaoa@essex.ac.uk>
License
GPL-2
Version
3.0

View on CRAN

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

Files in this package

enRich
enRich/src
enRich/src/MRF.c
enRich/src/MRFsrsp.c
enRich/src/MRFrep.c
enRich/src/MRFsp.c
enRich/NAMESPACE
enRich/data
enRich/data/p300cbp.200bp.rda
enRich/data/datalist
enRich/data/p300cbp.1000bp.rda
enRich/R
enRich/R/pprob.R
enRich/R/IPE.R
enRich/R/pprob_joint.R
enRich/R/enrich.mix.R
enRich/R/mixfit_offset.R
enRich/R/mrf_sp.R
enRich/R/mloglike_offsetNB.R
enRich/R/mix_single.R
enRich/R/NBlike_phi_offset.R
enRich/R/FDR.R
enRich/R/mrf_srsp.R
enRich/R/mix.R
enRich/R/mix.joint.R
enRich/R/mix_srsp1.R
enRich/R/mrf.joint.R
enRich/R/mix_offset.R
enRich/R/mloglike_offsetpois.R
enRich/R/mrf_single.R
enRich/R/enrich.mrf.R
enRich/R/mrf_rep.R
enRich/R/mrf.R
enRich/MD5
enRich/DESCRIPTION
enRich/man
enRich/man/mrf.Rd
enRich/man/mix.joint.Rd
enRich/man/mix.Rd
enRich/man/FDR.Rd
enRich/man/IPE.Rd
enRich/man/enrich.mrf.Rd
enRich/man/p300cbp.200bp.Rd
enRich/man/p300cbp.1000bp.Rd
enRich/man/enRich-package.Rd
enRich/man/mrf.joint.Rd
enRich/man/enrich.mix.Rd