bioc-issue-bot
commented
1 year ago Hi @richardheery
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: methodical
Title: Discovering genomic regions where methylation is strongly associated with transcriptional activity
Version: 0.99.0
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://support.bioconductor.org/tag/methodical
biocViews: DNAMethylation, Transcription, MethylationArray, Software
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.2
Depends:
GenomicRanges,
ggplot2,
R (>= 2.10),
SummarizedExperiment
LazyData: false
Imports:
Biostrings,
BSgenome,
cowplot,
data.table,
DelayedArray,
doParallel,
dplyr,
foreach,
GenomeInfoDb,
HDF5Array,
IRanges,
RcppRoll,
rhdf5,
rtracklayer,
S4Vectors,
scales,
tibble,
tidyr
Suggests:
AnnotationHub,
BSgenome.Athaliana.TAIR.TAIR9,
BSgenome.Hsapiens.UCSC.hg38,
knitr,
methrix,
rmarkdown
VignetteBuilder: knitr
lshep
richardheery
DarioS
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