The search feature on this website is currently unavailable.
To use google search type site: bioconductor.org "search term" in browser.

methodical

This is the development version of methodical; to use it, please install the devel version of Bioconductor.

Discovering genomic regions where methylation is strongly associated with transcriptional activity


Bioconductor version: Development (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 gmail.com>

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

Installation

To install this package, start R (version "4.4") 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")
calculating_methylation_transcription_correlations HTML R Script
identifying_tmrs HTML R Script
working_with_meth_rses HTML R Script
Reference Manual PDF
NEWS Text
INSTALL Text
LICENSE Text

Details

biocViews DNAMethylation, GenomeWideAssociation, MethylationArray, Software, Transcription
Version 0.99.25
In Bioconductor since BioC 3.19 (R-4.4)
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
URL https://github.com/richardheery/methodical
Bug Reports https://github.com/richardheery/methodical/issues
See More
Suggests AnnotationHub, annotatr, BiocStyle, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, DESeq2, knitr, methrix, rmarkdown, TumourMethData
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package methodical_0.99.25.tar.gz
Windows Binary
macOS Binary (x86_64) methodical_0.99.25.tgz
macOS Binary (arm64) methodical_0.99.24.tgz
Source Repository git clone https://git.bioconductor.org/packages/methodical
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/methodical
Bioc Package Browser https://code.bioconductor.org/browse/methodical/
Package Short Url https://bioconductor.org/packages/methodical/
Package Downloads Report Download Stats