Package: methylPipe 1.47.0

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:Mattia Pelizzola [aut], Kamal Kishore [aut], Mattia Furlan [ctb, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methylPipe/json (API)

# Install 'methylPipe' in R:

install.packages('methylPipe', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:methylPipe-1.47.0(bioc 3.24)methylPipe-1.46.0(bioc 3.23)

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

methylseq dnamethylation coverage sequencing

4.91 score 1 packages 1 scripts 9 mentions 32 exports 150 dependencies

Last updated from:a01817f3fb. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	283
linux-devel-arm64	WARNING	493
linux-devel-x86_64	WARNING	635
source / vignettes	OK	432
linux-release-arm64	WARNING	496
linux-release-x86_64	WARNING	645
macos-release-arm64	WARNING	390
macos-release-x86_64	WARNING	607
macos-oldrel-arm64	WARNING	369
macos-oldrel-x86_64	WARNING	879
windows-devel	WARNING	539
windows-release	WARNING	596
windows-oldrel	WARNING	539
wasm-release	OK	299

Exports:binC binmC binrC binscore binscore<-BSdata BSdataSet BSprepare chiCombP chr consolidateDMRs extractBinGRanges findDMR findPMDs GElist getCpos getCposChr getCposDensity mapBSdata2GRanges mapBSdata2GRangesBin mCsmoothing meth.call methstats nbins plotMeth pool.reads process.hmc profileDNAmetBin profileDNAmetBinParallel show splitChrs tabixdata2GR

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem caTools checkmate cigarillo cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gplots gridExtra gtable gtools Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle limma magrittr marray MASS Matrix MatrixGenerics matrixStats memoise mime nnet openssl pillar pkgconfig png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 XVector yaml

methylPipe

Rendered frommethylPipe.rnwusingknitr::knitr

Last update: 2015-05-11
Started: 2014-08-27

Citation

Development and contributors

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