methodical
This is the released version of methodical; for the devel version, see methodical.
Discovering genomic regions where methylation is strongly associated with transcriptional activity
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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
| Reference Manual | |
| NEWS | Text |
| INSTALL | Text |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, GenomeWideAssociation, MethylationArray, Software, Transcription |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | GPL (>= 3) |
| Depends | GenomicRanges, ggplot2, R (>= 4.0), SummarizedExperiment |
| Imports | AnnotationHub, BiocCheck, BiocManager, BiocParallel, BiocStyle, Biostrings, BSgenome, bsseq, 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 | |
| URL | https://github.com/richardheery/methodical |
| Bug Reports | https://github.com/richardheery/methodical/issues |
See More
| Suggests | rmarkdown |
| 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_1.8.0.tar.gz |
| Windows Binary (x86_64) | methodical_1.7.0.zip |
| macOS Binary (big-sur-x86_64) | methodical_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | methodical_1.8.0.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 |