MEDIPS: DNA IP-seq data analysis

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
Date of publicationNone
MaintainerLukas Chavez <l.chavez@dkfz.de>
LicenseGPL (>=2)
Version1.24.0

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

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