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Bioconductor - methodical (development version)

methodical

This is the development version of methodical; for the stable release version, see methodical.

Discovering genomic regions where methylation is strongly associated with transcriptional activity

Bioconductor version: Development (3.22)

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] ORCID: 0000-0001-8067-3114

Maintainer: Richard Heery <richardheery at gmail.com>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("methodical")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("methodical")

Details biocViews DNAMethylation, GenomeWideAssociation, MethylationArray, Software, Transcription Version 1.5.0 In Bioconductor since BioC 3.19 (R-4.4) (1 year) License GPL (>= 3) Depends GenomicRanges, ggplot2, R (>= 4.0), SummarizedExperiment Imports AnnotationHub, annotatr, BiocCheck, BiocManager, BiocParallel, BiocStyle, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, cowplot, data.table, DelayedArray, devtools, dplyr, ExperimentHub, foreach, GenomeInfoDb, HDF5Array, IRanges, knitr, MatrixGenerics, R.utils, rcmdcheck, RcppRoll, remotes, rhdf5, rtracklayer, S4Vectors, scales, tibble, tidyr, tools, TumourMethData, usethis System Requirements kallisto URL https://github.com/richardheery/methodical Bug Reports https://github.com/richardheery/methodical/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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