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Discovering genomic regions where methylation is strongly associated with transcriptional activity

Bioconductor version: Release (3.19)

DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.

Author: Richard Heery [aut, cre]

Maintainer: Richard Heery <richardheery at>

Citation (from within R, enter citation("methodical")):


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calculating_methylation_transcription_correlations HTML R Script
identifying_tmrs HTML R Script
working_with_meth_rses HTML R Script
Reference Manual PDF


biocViews DNAMethylation, GenomeWideAssociation, MethylationArray, Software, Transcription
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL (>= 3)
Depends GenomicRanges, ggplot2, R (>= 4.2.0), SummarizedExperiment
Imports BiocParallel, Biostrings, BSgenome, cowplot, data.table, DelayedArray, dplyr, ExperimentHub, foreach, GenomeInfoDb, HDF5Array, IRanges, R.utils, RcppRoll, rhdf5, rtracklayer, S4Vectors, scales, tibble, tidyr
System Requirements kallisto
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Suggests AnnotationHub, annotatr, BiocStyle, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, DESeq2, knitr, methrix, rmarkdown, TumourMethData
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