DESCRIPTION

Package: methodical
Title: Discovering genomic regions where methylation is strongly associated with transcriptional activity
Version: 1.1.0
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: 7.3.2
Depends: 
    GenomicRanges,
    ggplot2,
    R (>= 4.0),
    SummarizedExperiment
LazyData: false
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
Suggests: 
    BSgenome.Athaliana.TAIR.TAIR9,
    DESeq2,
    methrix,
    rmarkdown
VignetteBuilder: knitr
SystemRequirements: kallisto
URL: https://github.com/richardheery/methodical