Package: MEDIPS 1.59.0

Lukas Chavez

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.

Authors:Lukas Chavez, Matthias Lienhard, Joern Dietrich, Isaac Lopez Moyado

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MEDIPS.pdf |MEDIPS.html✨
MEDIPS/json (API)

# Install 'MEDIPS' in R:
install.packages('MEDIPS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:MEDIPS-1.59.0(bioc 3.21)MEDIPS-1.58.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dnamethylationcpgislanddifferentialexpressionsequencingchipseqpreprocessingqualitycontrolvisualizationmicroarraygeneticscoveragegenomeannotationcopynumbervariationsequencematching

5.17 score 74 scripts 322 downloads 89 mentions 57 exports 99 dependencies

Last updated 23 days agofrom:34d13453a3. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winNOTENov 19 2024
R-4.5-linuxNOTENov 19 2024
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R-4.4-macNOTENov 19 2024
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R-4.3-macNOTENov 19 2024

Exports:adjustReadsbin_numberbin.ROIschr_lengthschr_namesextendgenome_CFgenome_countgenome_namegetGRangegetMObjectFromWIGgetPairedGRangegetTypesmatDiffmatMaxmatMeanmatMinmatNnotNAmatSdmatTtestMEDIPS.addCNVMEDIPS.calibrationCurveMEDIPS.cnvMEDIPS.correlationMEDIPS.couplingVectorMEDIPS.CpGenrichMEDIPS.createROIsetMEDIPS.createSetMEDIPS.diffMethMEDIPS.exportWIGMEDIPS.GenomicCoordinatesMEDIPS.getAnnotationMEDIPS.getPositionsMEDIPS.mergeFramesMEDIPS.mergeSetsMEDIPS.methMEDIPS.plotCalibrationPlotMEDIPS.plotSaturationMEDIPS.plotSeqCoverageMEDIPS.rmsMEDIPS.saturationMEDIPS.selectROIsMEDIPS.selectSigMEDIPS.seqCoverageMEDIPS.setAnnotationnumber_patternnumber_regionspath_nameroissample_namescanBamToGRangesseq_patternsetTypesshiftedshowuniqwindow_size

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestDNAcopydplyredgeRfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluegtoolshmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngpreprocessCoreprettyunitsprogresspurrrR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxml2XVectoryamlzlibbioc

MEDIPS

Rendered fromMEDIPS.Rnwusingutils::Sweaveon Nov 19 2024.

Last update: 2018-08-30
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
(MeD)IP-seq data analysisMEDIPS-package MEDIPS
COUPLINGset class and internal functionschr_lengths,COUPLINGset-method chr_names,COUPLINGset-method COUPLINGset COUPLINGset-class genome_CF genome_CF,COUPLINGset-method genome_name,COUPLINGset-method number_pattern number_pattern,COUPLINGset-method seq_pattern seq_pattern,COUPLINGset-method show,COUPLINGset-method window_size,COUPLINGset-method
Function to run a copy number variation analysis.MEDIPS.addCNV
Calculates pairwise Pearson correlations between provided MEDIPS SETsMEDIPS.correlation
Calculates the sequence pattern densities at genome wide windows.MEDIPS.couplingVector
Calculates CpG enrichment of provided short reads compared to the reference genome.MEDIPS.CpGenrich
Creates a MEDIPS ROI SET by reading a suitable input filebin.ROIs MEDIPS.createROIset
Creates a MEDIPS SET by reading a suitable input filegetMObjectFromWIG getPairedGRange MEDIPS.createSet readRegionsFile scanBamToGRanges
Exports count, rpkm, or sequence pattern densities into a wiggle file.MEDIPS.exportWIG
Funtion to fetch annotations from biomaRt.MEDIPS.getAnnotation
Merges genomic coordinates of neighboring windows into one supersized windowMEDIPS.mergeFrames
Creates one merged MEDIPS SET out of two.MEDIPS.mergeSets
Funtion summarizes coverage profiles for given MEDIPS SETs and allows to calculate differental coverage and copy number vartiation, if applicable.MEDIPS.diffMeth MEDIPS.meth
Creates the calibration plot.MEDIPS.plotCalibrationPlot
Function plots the results of the MEDIPS.saturationAnalysis function.MEDIPS.plotSaturation
Function plots the results of the MEDIPS.seqCoverage function.MEDIPS.plotSeqCoverage
Function calculates the saturation/reproducibility of the provided IP-Seq data.MEDIPS.saturation
Selects row-wise subsets of a result table as returned by the MEDIPS.meth function.MEDIPS.selectROIs
Selects windows which show significant differential coverage between two MEDIPS SETs from a resultTable (as returned by the function MEDIPS.meth).MEDIPS.selectSig
The function identifies the number of CpGs (or any other predefined sequence pattern) covered by the given short reads.MEDIPS.seqCoverage
Funtion to annotate a matrix of genomic coordinates (i.e. a result table) by a given annotation object.MEDIPS.setAnnotation
MEDIPSroiSet class and internal functionsbin_number bin_number,MEDIPSroiSet-method chr_lengths,MEDIPSroiSet-method chr_names,MEDIPSroiSet-method extend,MEDIPSroiSet-method genome_count,MEDIPSroiSet-method genome_name,MEDIPSroiSet-method MEDIPSroiSet MEDIPSroiSet-class number_regions,MEDIPSroiSet-method path_name,MEDIPSroiSet-method ROI,MEDIPSroiSet-method rois rois,MEDIPSroiSet-method sample_name,MEDIPSroiSet-method shifted,MEDIPSroiSet-method show,MEDIPSroiSet-method uniq,MEDIPSroiSet-method
MEDIPSset class and internal functionsadjustReads bin_size bin_size,MEDIPSset-method chr_lengths chr_lengths,MEDIPSset-method chr_names chr_names,MEDIPSset-method extend extend,MEDIPSset-method genome_count genome_count,MEDIPSset-method genome_name genome_name,MEDIPSset-method getGRange getTypes matDiff matMax matMean matMin matNnotNA matSd matTtest MEDIPS.Bam2GRanges MEDIPS.Bed2Granges MEDIPS.calibrationCurve MEDIPS.cnv MEDIPS.GenomicCoordinates MEDIPS.getPositions MEDIPS.rms MEDIPSset MEDIPSset-class number_regions number_regions,MEDIPSset-method path_name path_name,MEDIPSset-method sample_name sample_name,MEDIPSset-method setTypes shifted shifted,MEDIPSset-method show show,MEDIPSset-method uniq uniq,MEDIPSset-method window_size window_size,MEDIPSset-method