MEDIPS: DNA IP-seq data analysis
Version 1.28.0

MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.

AuthorLukas Chavez, Matthias Lienhard, Joern Dietrich, Isaac Lopez Moyado
Bioconductor views ChIPSeq CopyNumberVariation Coverage CpGIsland DNAMethylation DifferentialExpression Genetics GenomeAnnotation Microarray Preprocessing QualityControl SequenceMatching Sequencing Visualization
Date of publicationNone
MaintainerLukas Chavez <l.chavez@dkfz.de>
LicenseGPL (>=2)
Version1.28.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MEDIPS")

Getting started

Package overview

Popular man pages

MEDIPS.CpGenrich: Calculates CpG enrichment of provided short reads compared to...
MEDIPS.createSet: Creates a MEDIPS SET by reading a suitable input file
MEDIPS.exportWIG: Exports count, rpkm, or sequence pattern densities into a...
MEDIPS.getAnnotation: Funtion to fetch annotations from biomaRt.
MEDIPS.meth: Funtion summarizes coverage profiles for given MEDIPS SETs...
MEDIPS.plotCalibrationPlot: Creates the calibration plot.
MEDIPS.saturation: Function calculates the saturation/reproducibility of the...
See all...

All man pages Function index File listing

Man pages

COUPLINGset-class: COUPLINGset class and internal functions
MEDIPS.addCNV: Function to run a copy number variation analysis.
MEDIPS.correlation: Calculates pairwise Pearson correlations between provided...
MEDIPS.couplingVector: Calculates the sequence pattern densities at genome wide...
MEDIPS.CpGenrich: Calculates CpG enrichment of provided short reads compared to...
MEDIPS.createROIset: Creates a MEDIPS ROI SET by reading a suitable input file
MEDIPS.createSet: Creates a MEDIPS SET by reading a suitable input file
MEDIPS.exportWIG: Exports count, rpkm, or sequence pattern densities into a...
MEDIPS.getAnnotation: Funtion to fetch annotations from biomaRt.
MEDIPS.mergeFrames: Merges genomic coordinates of neighboring windows into one...
MEDIPS.mergeSets: Creates one merged MEDIPS SET out of two.
MEDIPS.meth: Funtion summarizes coverage profiles for given MEDIPS SETs...
MEDIPS-package: (MeD)IP-seq data analysis
MEDIPS.plotCalibrationPlot: Creates the calibration plot.
MEDIPS.plotSaturation: Function plots the results of the MEDIPS.saturationAnalysis...
MEDIPS.plotSeqCoverage: Function plots the results of the MEDIPS.seqCoverage...
MEDIPSroiSet-class: MEDIPSroiSet class and internal functions
MEDIPS.saturation: Function calculates the saturation/reproducibility of the...
MEDIPS.selectROIs: Selects row-wise subsets of a result table as returned by the...
MEDIPS.selectSig: Selects windows which show significant differential coverage...
MEDIPS.seqCoverage: The function identifies the number of CpGs (or any other...
MEDIPS.setAnnotation: Funtion to annotate a matrix of genomic coordinates (i.e. a...
MEDIPSset-class: MEDIPSset class and internal functions

Functions

Files

DESCRIPTION
NAMESPACE
R
R/MEDIPS-classes.R
R/MEDIPS.CpGenrich.R
R/MEDIPS.GenomicCoordinates.R
R/MEDIPS.annotate.R
R/MEDIPS.calibrationCurve.R
R/MEDIPS.cnv.R
R/MEDIPS.correlation.R
R/MEDIPS.couplingVector.R
R/MEDIPS.createROIset.R
R/MEDIPS.createSet.R
R/MEDIPS.diffMeth.R
R/MEDIPS.exportWIG.R
R/MEDIPS.functions.R
R/MEDIPS.getPositions.R
R/MEDIPS.mergeFrames.R
R/MEDIPS.mergeSets.R
R/MEDIPS.meth.R
R/MEDIPS.plotCalibrationPlot.R
R/MEDIPS.plotSaturation.R
R/MEDIPS.plotSeqCoverage.R
R/MEDIPS.readRegionsFile.R
R/MEDIPS.rms.R
R/MEDIPS.saturation.R
R/MEDIPS.selectROIs.R
R/MEDIPS.selectSig.R
R/MEDIPS.seqCoverage.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/MEDIPS.R
inst/doc/MEDIPS.Rnw
inst/doc/MEDIPS.pdf
inst/extdata
man
man/COUPLINGset-class.Rd
man/MEDIPS-package.Rd
man/MEDIPS.CpGenrich.Rd
man/MEDIPS.addCNV.Rd
man/MEDIPS.correlation.Rd
man/MEDIPS.couplingVector.Rd
man/MEDIPS.createROIset.Rd
man/MEDIPS.createSet.Rd
man/MEDIPS.exportWIG.Rd
man/MEDIPS.getAnnotation.Rd
man/MEDIPS.mergeFrames.Rd
man/MEDIPS.mergeSets.Rd
man/MEDIPS.meth.Rd
man/MEDIPS.plotCalibrationPlot.Rd
man/MEDIPS.plotSaturation.Rd
man/MEDIPS.plotSeqCoverage.Rd
man/MEDIPS.saturation.Rd
man/MEDIPS.selectROIs.Rd
man/MEDIPS.selectSig.Rd
man/MEDIPS.seqCoverage.Rd
man/MEDIPS.setAnnotation.Rd
man/MEDIPSroiSet-class.Rd
man/MEDIPSset-class.Rd
vignettes
vignettes/MEDIPS.Rnw
vignettes/MEDIPSTutorial.bib
MEDIPS documentation built on May 20, 2017, 10:47 p.m.

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