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

Functions

adjustReads Man page
bin_number Man page
bin_number,MEDIPSroiSet-method Man page
bin.ROIs Man page
bin_size Man page
bin_size,MEDIPSset-method Man page
chr_lengths Man page
chr_lengths,COUPLINGset-method Man page
chr_lengths,MEDIPSroiSet-method Man page
chr_lengths,MEDIPSset-method Man page
chr_names Man page
chr_names,COUPLINGset-method Man page
chr_names,MEDIPSroiSet-method Man page
chr_names,MEDIPSset-method Man page
COUPLINGset Man page
COUPLINGset-class Man page
extend Man page
extend,MEDIPSroiSet-method Man page
extend,MEDIPSset-method Man page
genome_CF Man page
genome_CF,COUPLINGset-method Man page
genome_count Man page
genome_count,MEDIPSroiSet-method Man page
genome_count,MEDIPSset-method Man page
genome_name Man page
genome_name,COUPLINGset-method Man page
genome_name,MEDIPSroiSet-method Man page
genome_name,MEDIPSset-method Man page
getGRange Man page
getMObjectFromWIG Man page
getPairedGRange Man page
getTypes Man page
matDiff Man page
matMax Man page
matMean Man page
matMin Man page
matNnotNA Man page
matSd Man page
matTtest Man page
MEDIPS Man page
MEDIPS.addCNV Man page
MEDIPS.Bam2GRanges Man page
MEDIPS.Bed2Granges Man page
MEDIPS.calibrationCurve Man page
MEDIPS.cnv Man page
MEDIPS.correlation Man page
MEDIPS.couplingVector Man page
MEDIPS.CpGenrich Man page
MEDIPS.createROIset Man page
MEDIPS.createSet Man page
MEDIPS.diffMeth Man page
MEDIPS.exportWIG Man page
MEDIPS.GenomicCoordinates Man page
MEDIPS.getAnnotation Man page
MEDIPS.getPositions Man page
MEDIPS.mergeFrames Man page
MEDIPS.mergeSets Man page
MEDIPS.meth Man page
MEDIPS-package Man page
MEDIPS.plotCalibrationPlot Man page
MEDIPS.plotSaturation Man page
MEDIPS.plotSeqCoverage Man page
MEDIPS.rms Man page
MEDIPSroiSet Man page
MEDIPSroiSet-class Man page
MEDIPS.saturation Man page
MEDIPS.selectROIs Man page
MEDIPS.selectSig Man page
MEDIPS.seqCoverage Man page
MEDIPSset Man page
MEDIPS.setAnnotation Man page
MEDIPSset-class Man page
number_pattern Man page
number_pattern,COUPLINGset-method Man page
number_regions Man page
number_regions,MEDIPSroiSet-method Man page
number_regions,MEDIPSset-method Man page
path_name Man page
path_name,MEDIPSroiSet-method Man page
path_name,MEDIPSset-method Man page
readRegionsFile Man page
ROI,MEDIPSroiSet-method Man page
rois Man page
rois Man page
rois,MEDIPSroiSet-method Man page
sample_name Man page
sample_name,MEDIPSroiSet-method Man page
sample_name,MEDIPSset-method Man page
scanBamToGRanges Man page
seq_pattern Man page
seq_pattern,COUPLINGset-method Man page
setTypes Man page
shifted Man page
shifted,MEDIPSroiSet-method Man page
shifted,MEDIPSset-method Man page
show Man page
show,COUPLINGset-method Man page
show,MEDIPSroiSet-method Man page
show,MEDIPSset-method Man page
uniq Man page
uniq,MEDIPSroiSet-method Man page
uniq,MEDIPSset-method Man page
window_size Man page
window_size,COUPLINGset-method Man page
window_size,MEDIPSset-method Man page

Files

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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