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:
MEDIPS_1.59.0.tar.gz
MEDIPS_1.59.0.zip(r-4.5)MEDIPS_1.59.0.zip(r-4.4)MEDIPS_1.59.0.zip(r-4.3)
MEDIPS_1.59.0.tgz(r-4.4-any)MEDIPS_1.59.0.tgz(r-4.3-any)
MEDIPS_1.59.0.tar.gz(r-4.5-noble)MEDIPS_1.59.0.tar.gz(r-4.4-noble)
MEDIPS_1.59.0.tgz(r-4.4-emscripten)MEDIPS_1.59.0.tgz(r-4.3-emscripten)
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')) |
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
Last updated 2 months agofrom:34d13453a3. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | NOTE | Dec 19 2024 |
| R-4.5-linux | NOTE | Dec 19 2024 |
| R-4.4-win | NOTE | Dec 19 2024 |
| R-4.4-mac | NOTE | Dec 19 2024 |
| R-4.3-win | NOTE | Dec 19 2024 |
| R-4.3-mac | NOTE | Dec 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
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| (MeD)IP-seq data analysis | MEDIPS-package MEDIPS |
| COUPLINGset class and internal functions | chr_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 SETs | MEDIPS.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 file | bin.ROIs MEDIPS.createROIset |
| Creates a MEDIPS SET by reading a suitable input file | getMObjectFromWIG 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 window | MEDIPS.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 functions | bin_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 functions | adjustReads 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 |
