methyvim
This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see methyvimData.
Differential Methylation Analysis with Targeted Minimum Loss-Based Estimates of Variable Importance Measures
Bioconductor version: 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("methyvim")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("methyvim")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
| LICENSE | Text |
Details
| biocViews | Clustering, DNAMethylation, DifferentialMethylation, MethylSeq, MethylationArray, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| 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 |
| System Requirements | |
| URL | https://github.com/nhejazi/methyvim |
| Bug Reports | https://github.com/nhejazi/methyvim/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth, nnet, gam, arm, snow, parallel, BatchJobs, minfiData, methyvimData |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
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 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methyvim |
| Package Short Url | https://bioconductor.org/packages/methyvim/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |