methodical
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 gmail.com>
citation("methodical")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| INSTALL | Text | |
| LICENSE | Text |
Details
| 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 |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | methodical_1.0.0.tgz |
| macOS Binary (arm64) | methodical_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/methodical |
| Source Repository (Developer Access) | git clone [email protected]:packages/methodical |
| Bioc Package Browser | https://code.bioconductor.org/browse/methodical/ |
| Package Short Url | https://bioconductor.org/packages/methodical/ |
| Package Downloads Report | Download Stats |