Package: methyvim
Title: Targeted, Robust, and Model-free Differential Methylation
        Analysis
Version: 1.11.0
Authors@R: c(
  person("Nima", "Hejazi", email = "nh@nimahejazi.org",
         role = c("aut", "cre", "cph"),
         comment = c(ORCID = "0000-0002-7127-2789")),
  person("Rachael", "Phillips", email = "rachaelvphillips@berkeley.edu",
         role = "ctb",
         comment = c(ORCID = "0000-0002-8474-591X")),
  person("Mark", "van der Laan", email = "laan@stat.berkeley.edu",
         role = c("aut", "ths"),
         comment = c(ORCID = "0000-0003-1432-5511")),
  person("Alan", "Hubbard", email = "hubbard@berkeley.edu",
         role = c("ctb", "ths"),
         comment = c(ORCID = "0000-0002-3769-0127"))
  )
Description: This package provides facilities for differential methylation
  analysis based on variable importance measures (VIMs), a class of statistical
  target parameters that arise in causal inference. The estimation and inference
  procedures provided are nonparametric, relying on ensemble machine learning to
  flexibly assess functional relationships among covariates and the outcome of
  interest. These tools can be applied to differential methylation at the level
  of CpG sites, to obtain valid statistical inference even after corrections for
  multiple hypothesis testing.
Depends: R (>= 3.4.0)
License: file LICENSE
URL: https://github.com/nhejazi/methyvim
BugReports: https://github.com/nhejazi/methyvim/issues
Encoding: UTF-8
Imports: stats, cluster, methods, ggplot2, ggsci, gridExtra, superheat,
        dplyr, gtools, tmle (>= 1.4.0.1), future, doFuture, S4Vectors,
        BiocGenerics, BiocParallel, SummarizedExperiment, GenomeInfoDb,
        bumphunter, IRanges, limma, minfi
Suggests: testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth,
        nnet, gam, arm, snow, parallel, BatchJobs, minfiData,
        methyvimData
VignetteBuilder: knitr
RoxygenNote: 7.0.2
biocViews: Clustering, DNAMethylation, DifferentialMethylation,
        MethylationArray, MethylSeq
git_url: https://git.bioconductor.org/packages/methyvim
git_branch: master
git_last_commit: 7b4ee9f
git_last_commit_date: 2020-04-27
Date/Publication: 2020-04-27
NeedsCompilation: no
Packaged: 2020-04-28 03:52:41 UTC; biocbuild
Author: Nima Hejazi [aut, cre, cph] (<https://orcid.org/0000-0002-7127-2789>),
  Rachael Phillips [ctb] (<https://orcid.org/0000-0002-8474-591X>),
  Mark van der Laan [aut, ths] (<https://orcid.org/0000-0003-1432-5511>),
  Alan Hubbard [ctb, ths] (<https://orcid.org/0000-0002-3769-0127>)
Maintainer: Nima Hejazi <nh@nimahejazi.org>
Built: R 4.0.0; ; 2020-04-28 14:26:10 UTC; windows
