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 |

**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

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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