methyvim
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see methyvimData.
Targeted, Robust, and Model-free Differential Methylation Analysis
Bioconductor version: 3.9
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], Mark van der Laan [aut, ths], Alan Hubbard [ctb, ths], Rachael Phillips [ctb]
Maintainer: Nima Hejazi <nhejazi at berkeley.edu>
citation("methyvim")):
Installation
To install this package, start R (version "3.6") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("methyvim")| Targeted Data-Adaptive Estimation and Inference for Differential Methylation Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, DNAMethylation, DifferentialMethylation, MethylSeq, MethylationArray, Software |
| Version | 1.6.0 |
| 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, ggsci, gridExtra, superheat, dplyr, gtools, tmle, future, doFuture, S4Vectors, BiocGenerics, BiocParallel, 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_1.6.0.tar.gz |
| Windows Binary | methyvim_1.6.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | methyvim_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/methyvim |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methyvim |
| Bioc Package Browser | https://code.bioconductor.org/browse/methyvim/ |
| Package Short Url | https://bioconductor.org/packages/methyvim/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |