Package: methylPipe 1.41.0
Mattia Furlan
methylPipe: Base resolution DNA methylation data analysis
Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.
Authors:
methylPipe_1.41.0.tar.gz
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methylPipe.pdf |methylPipe.html✨
methylPipe/json (API)
NEWS
| # Install 'methylPipe' in R: |
| install.packages('methylPipe', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:methylPipe-1.41.0(bioc 3.21)methylPipe-1.40.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
methylseqdnamethylationcoveragesequencing
Last updated 2 months agofrom:9ff081a1f7. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 29 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 29 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 29 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 29 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 29 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 29 2024 |
| R-4.3-mac-x86_64 | WARNING | Nov 29 2024 |
| R-4.3-mac-aarch64 | WARNING | Nov 29 2024 |
Exports:binCbinmCbinrCbinscorebinscore<-BSdataBSdataSetBSpreparechiCombPchrconsolidateDMRsextractBinGRangesfindDMRfindPMDsGElistgetCposgetCposChrgetCposDensitymapBSdata2GRangesmapBSdata2GRangesBinmCsmoothingmeth.callmethstatsnbinsplotMethpool.readsprocess.hmcprofileDNAmetBinprofileDNAmetBinParallelshowsplitChrstabixdata2GR
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcaToolscheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegplotsgridExtragtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmamagrittrmarrayMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Analysis of base-pair resolution DNA methylation data. | methylPipe-package methylPipe |
| Class "BSdata" | BSdata BSdata-class show,BSdata-method |
| Class "BSdataSet" | $,BSdataSet $,BSdataSet-method BSdataSet BSdataSet-class length,BSdataSet-method show,BSdataSet-method [,BSdataSet,ANY,ANY-method [[,BSdataSet,ANY,ANY-method [[<-,BSdataSet,ANY,ANY-method |
| Preparing tabular data to be used to feed a BSdata object | BSprepare |
| Fisher's method implementation | chiCombP |
| Consolidating Differentially Methylated Regions (DMRs) | consolidateDMRs |
| Extract genomic ranges for a given bin | extractBinGRanges |
| Identifying Differentially Methylated Regions (DMRs) | findDMR findDMR,BSdataSet-method findDMR,methylPipe,BSdataSet findDMR,methylPipe,BSdataSet-method findDMR-methods |
| Identifying Partially Methylated Domains (PMDs) | findPMDs findPMDs,BSdata-method findPMDs,methylPipe,BSdata findPMDs,methylPipe,BSdata-method findPMDs-methods |
| Class "GEcollection" | binC binC,GEcollection-method binmC binmC,GEcollection-method binrC binrC,GEcollection-method binscore binscore,GEcollection-method binscore<- binscore<-,GEcollection-method chr chr,GEcollection-method GEcollection GEcollection-class length length,GEcollection-method nbins nbins,GEcollection-method show,GEcollection-method |
| Class "GElist" | $,GElist $,GElist-method GElist GElist-class length,GElist-method show,GElist-method [,GElist,ANY,ANY-method [[,GElist,ANY,ANY-method [[<-,GElist,ANY,ANY-method |
| Get genomic Cxx positons for a series of genomic regions | getCpos getCposChr |
| Determines the density of genomic Cxx positions for a series of genomic regions | getCposDensity |
| Retrieve mC calls for a GRanges set of genomic regions given a BSdata object for a sample | mapBSdata2GRanges mapBSdata2GRangesBin |
| Smoothing and plotting methylation data | mCsmoothing mCsmoothing,BSdata-method mCsmoothing,methylPipe,BSdata mCsmoothing,methylPipe,BSdata-method mCsmoothing-methods |
| Function to read methylation calls | meth.call |
| Exploratory statistics of samples in BSdataSet object | methstats methstats,BSdataSet-method methstats,methylPipe,BSdataSet methstats,methylPipe,BSdataSet-method methstats-methods |
| Plot DNA methylation together with other omics, or annotation data for a genomic region | plotMeth |
| Function to pool reads of replicates | pool.reads |
| Processing hmC information from the MLML output | process.hmc |
| Profile DNA methylation data for a set of genomic regions | profileDNAmetBin profileDNAmetBinParallel |
| Partitioning genome in chunks, for parallel computation | splitChrs |
| Convert the list returned by the function scanTabix into a GRanges | tabixdata2GR |