iChip: Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models

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This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. It can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.

Author
Qianxing Mo
Date of publication
None
Maintainer
Qianxing Mo <qmo@bcm.edu>
License
GPL (>= 2)
Version
1.28.0

View on Bioconductor

Man pages

enrichreg
Call and merge enriched probes to enriched regions.
iChip1
Bayesian modeling of ChIP-chip data through hidden Ising...
iChip2
Bayesian modeling of ChIP-chip data through hidden Ising...
lmtstat
A wrapper function used to calculated the limma t-statistics
oct4
Oct4 data
p53
p53 data

Files in this package

iChip/DESCRIPTION
iChip/NAMESPACE
iChip/R
iChip/R/iChip.R
iChip/build
iChip/build/vignette.rds
iChip/data
iChip/data/oct4.rda
iChip/data/p53.rda
iChip/demo
iChip/demo/00Index
iChip/demo/iChipdemo.R
iChip/inst
iChip/inst/doc
iChip/inst/doc/iChip.R
iChip/inst/doc/iChip.Rnw
iChip/inst/doc/iChip.pdf
iChip/man
iChip/man/enrichreg.Rd
iChip/man/iChip1.Rd
iChip/man/iChip2.Rd
iChip/man/lmtstat.Rd
iChip/man/oct4.Rd
iChip/man/p53.Rd
iChip/src
iChip/src/iChip.c
iChip/vignettes
iChip/vignettes/iChip.Rnw