MEDIPS: DNA IP-seq data analysis

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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.

Author
Lukas Chavez, Matthias Lienhard, Joern Dietrich, Isaac Lopez Moyado
Date of publication
None
Maintainer
Lukas Chavez <l.chavez@dkfz.de>
License
GPL (>=2)
Version
1.24.0

View on Bioconductor

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

Files in this package

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