Bioconductor version: Release (3.6)
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 relationship among covariates and the outcome of interest. These tools can be applied to differential methylation at the level of CpG sites, with valid inference after multiple hypothesis testing.
Author: Nima Hejazi [aut, cre, cph], Rachael Phillips [ctb], Alan Hubbard [ctb], Mark van der Laan [aut]
Maintainer: Nima Hejazi <nhejazi at berkeley.edu>
Citation (from within R,
enter citation("methyvim")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("methyvim")
HTML | R Script | methyvim: Variable Importance for DNA Methylation |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | Clustering, DNAMethylation, DifferentialMethylation, MethylSeq, MethylationArray, Software |
Version | 1.0.0 |
License | file LICENSE |
Depends | R (>= 3.4.0) |
Imports | stats, cluster, methods, ggplot2, gridExtra, superheat, wesanderson, magrittr, dplyr, gtools, tmle, future, doFuture, BiocParallel, BiocGenerics, SummarizedExperiment, GenomeInfoDb, bumphunter, IRanges, limma, minfi |
LinkingTo | |
Suggests | testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth, nnet, gam, arm, snow, parallel, BatchJobs, minfiData, methyvimData |
SystemRequirements | |
Enhances | |
URL | https://github.com/nhejazi/methyvim |
BugReports | https://github.com/nhejazi/methyvim/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | methyvim_1.0.0.tar.gz |
Windows Binary | methyvim_1.0.0.zip |
Mac OS X 10.11 (El Capitan) | methyvim_1.0.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/methyvim |
Package Short Url | http://bioconductor.org/packages/methyvim/ |
Package Downloads Report | Download Stats |
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