Package: methyvim
Title: Targeted, Robust, and Model-free Differential Methylation
        Analysis
Version: 1.4.0
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"))
  )
Maintainer: Nima Hejazi <nhejazi@berkeley.edu>
Author: Nima Hejazi [aut, cre, cph], Mark van der Laan [aut, ths], Alan Hubbard
  [ctb, ths], Rachael Phillips [ctb]
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, 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: 6.1.0.9000
biocViews: Clustering, DNAMethylation, DifferentialMethylation,
        MethylationArray, MethylSeq
git_url: https://git.bioconductor.org/packages/methyvim
git_branch: RELEASE_3_8
git_last_commit: 13eae51
git_last_commit_date: 2018-10-30
Date/Publication: 2018-10-30
NeedsCompilation: no
Packaged: 2018-10-31 03:48:46 UTC; biocbuild
Built: R 3.5.1; ; 2018-10-31 11:29:53 UTC; windows
