MeDiChI: MeDiChI ChIP-chip deconvolution library
Version 0.4.0

Model-based deconvolution of genome-wide binding (ChIP-chip) data

Browse man pages Browse package API and functions Browse package files

AuthorDavid J Reiss
Date of publicationNone
MaintainerDavid J Reiss <dreiss@systemsbiology.org>
LicenseGPL-2
Version0.4.0
URL http://baliga.systemsbiology.net/medichi
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MeDiChI", repos="http://R-Forge.R-project.org")

Man pages

chip.deconv: High-resolution model-based deconvolution of normalized...
deconv.entire.genome: High-resolution model-based deconvolution of normalized...
fit.peak.profile: Iteratively learn deconvolution kernel (peak profile) from...
generate.binding.profile: Construct the binding profile ('kernel') required as input...
generate.fake.data: Generate simulated ChIP-chip data.
MeDiChI-data: ChIP-chip data supporting the MeDiChI package
MeDiChI-package: MeDiChI ChIP-chip deconvolution library

Functions

MeDiChI Man page
MeDiChI-data Man page
MeDiChI-package Man page
chip.deconv Man page Source code
coef.chip.deconv Man page Source code
coef.chip.deconv.entire.genome Man page Source code
convolve.func Source code
data.halo.hires Man page
data.halo.lowres Man page
data.yeast.gcn4 Man page
deconv.entire.genome Man page Source code
fit.peak.profile Man page Source code
gene.coords Man page
generate.binding.profile Man page Source code
generate.fake.data Man page Source code
get.biggest.peaks Source code
get.chip.boot.probs Source code
get.peak.profile Source code
kernel.halo.hires Man page
kernel.halo.lowres Man page
kernel.yeast.gcn4 Man page
kernel.yeast.gcn4.jbd Man page
lars.pos Source code
load.chip.data Source code
make.predictor.matrix Source code
my.drop Source code
nnls.lars.faster Source code
onLoad Source code
plot.chip.deconv Man page Source code
plot.chip.deconv.entire.genome Man page Source code
plot.fit.peak.profile Man page Source code
plot.genes.in.window Source code
post.proc.coeffs Source code
post.proc.deconv Source code
print.chip.deconv Man page Source code
print.chip.deconv.entire.genome Man page Source code
updateR.faster Source code

Files

data
data/datalist
data/halo.hires.rda
data/halo.lowres.rda
data/yeast.gcn4.rda
R
R/chip.deconv.pkg.R
NAMESPACE
inst
inst/doc
inst/doc/peakprofile.png
inst/doc/MeDiChI.pdf
inst/doc/MeDiChI.Rnw
DESCRIPTION
man
man/generate.fake.data.Rd
man/chip.deconv.Rd
man/generate.binding.profile.Rd
man/MeDiChI-package.Rd
man/MeDiChI-data.Rd
man/fit.peak.profile.Rd
man/deconv.entire.genome.Rd
demo
demo/MeDiChI.R
demo/00Index
MeDiChI documentation built on May 21, 2017, 1:31 a.m.