DOI: 10.18129/B9.bioc.methyvim    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see methyvim.

Targeted, Robust, and Model-free Differential Methylation Analysis

Bioconductor version: 3.10

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.

Author: Nima Hejazi [aut, cre, cph] , Rachael Phillips [ctb] , Mark van der Laan [aut, ths] , Alan Hubbard [ctb, ths]

Maintainer: Nima Hejazi <nh at>

Citation (from within R, enter citation("methyvim")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Targeted Data-Adaptive Estimation and Inference for Differential Methylation Analysis
PDF   Reference Manual
Text   NEWS


biocViews Clustering, DNAMethylation, DifferentialMethylation, MethylSeq, MethylationArray, Software
Version 1.8.0
In Bioconductor since BioC 3.6 (R-3.4) (2.5 years)
License file LICENSE
Depends R (>= 3.4.0)
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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package methyvim_1.8.0.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) methyvim_1.8.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: