Package: methodical
Title: Discovering genomic regions where methylation is strongly
        associated with transcriptional activity
Version: 0.99.21
Authors@R: 
    person("Richard", "Heery", , "richardheery@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-8067-3114"))
Description: 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. 
License: GPL (>= 3)
BugReports: https://github.com/richardheery/methodical/issues
biocViews: DNAMethylation, MethylationArray, Transcription,
        GenomeWideAssociation, Software
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends: GenomicRanges, ggplot2, R (>= 4.3.0), SummarizedExperiment
LazyData: false
Imports: BiocParallel, Biostrings, BSgenome, cowplot, data.table,
        DelayedArray, dplyr, ExperimentHub, foreach, GenomeInfoDb,
        HDF5Array, IRanges, R.utils, RcppRoll, rhdf5, rtracklayer,
        S4Vectors, scales, tibble, tidyr
Suggests: AnnotationHub, annotatr, BiocStyle,
        BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Hsapiens.UCSC.hg38, DESeq2, knitr, methrix, rmarkdown,
        TCGAbiolinks, TumourMethData
VignetteBuilder: knitr
SystemRequirements: kallisto
URL: https://github.com/richardheery/methodical
git_url: https://git.bioconductor.org/packages/methodical
git_branch: devel
git_last_commit: 9cc9fff
git_last_commit_date: 2024-01-12
Repository: Bioconductor 3.19
Date/Publication: 2024-01-14
NeedsCompilation: no
Packaged: 2024-01-14 23:02:07 UTC; biocbuild
Author: Richard Heery [aut, cre] (<https://orcid.org/0000-0001-8067-3114>)
Maintainer: Richard Heery <richardheery@gmail.com>
