RAMEN/DESCRIPTION at main · ropensci/RAMEN · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
Package: RAMEN
Title: Regional Association of Methylome variability with the Exposome and geNome
Version: 2.99.0
Authors@R: c(
    person("Erick I.", "Navarro-Delgado",
            email = "erick.delgado@ubc.ca",
            role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1040-3519")),
    person("Keegan", "Korthauer",
            role = "aut",
            email = "keegan@stat.ubc.ca",
            comment = c(ORCID = "0000-0002-4565-1654")),
    person("Michael S.", "Kobor",
            email = "michael.kobor@ubc.ca",
            role = "aut",
            comment = c(ORCID = "0000-0003-4140-1743")),
    person("Lluís", "Revilla Sancho",
            email = "lluis.revilla@gmail.com",
            role = "rev",
            comment = c(ORCID = "0000-0001-9747-2570")),
    person("Ulduz", "Vafadarshamasbi",
            email = "vafadar.u@uq.edu.au",
            role = "rev",
            comment = c(ORCID = "0000-0002-8370-8084")),
    person("The University of British Columbia", role = "fnd")
            )
Description: RAMEN is an R package which goal is to identify Variable Methylated Loci (VML) in microarray DNA methylation data and then, using genome and exposome data, identify which individual genetic (G) or environmental (E) or joint (G+E or GxE) model better explains the VML variability. This package provides estimates of genetic and environmental contribution for each VML, allowing researchers to gain insights into the complex interplay between genetics, environment and DNA methylation.
License: GPL (>= 3)
Encoding: UTF-8
biocViews: DNAMethylation, GenomeWideAssociation, Epigenetics, Regression, SNP, Microarray, MethylationArray, GeneticVariability
Roxygen: list(markdown = TRUE)
Suggests:
    BiocStyle,
    knitr,
    magick,
    rmarkdown,
    ggplot2,
    tidyr,
    doParallel,
    IlluminaHumanMethylation450kanno.ilmn12.hg19,
    IlluminaHumanMethylationEPICv2anno.20a1.hg38,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports:
    doRNG,
    dplyr,
    foreach,
    GenomicRanges,
    glmnet,
    IRanges,
    matrixStats,
    methods,
    relaimpo,
    S4Vectors,
    IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
    stats
VignetteBuilder: knitr
Depends:
    R (>= 4.6.0)
LazyData: true
URL:
    https://ropensci.github.io/RAMEN/ ,
    https://github.com/ropensci/RAMEN/
BugReports: https://github.com/ropensci/RAMEN/issues
Config/roxygen2/version: 8.1.0