methyAnalysis
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 methyAnalysis.
DNA methylation data analysis and visualization
Bioconductor version: 3.9
The methyAnalysis package aims for the DNA methylation data analysis and visualization. A MethyGenoSet class is defined to keep the chromosome location information together with the data. The package also includes functions of estimating the methylation levels from Methy-Seq data.
Author: Pan Du, Richard Bourgon
Maintainer: Pan Du <dupan.mail at gmail.com>, Lei Huang <lhuang at bsd.uchicago.edu>, Gang Feng <g-feng at northwestern.edu>
citation("methyAnalysis")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("methyAnalysis")
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("methyAnalysis")| An Introduction to the methyAnalysis package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Microarray, Software, Visualization |
| Version | 1.26.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb, GenomicRanges, Biobase(>= 2.34.0), org.Hs.eg.db |
| Imports | grDevices, stats, utils, lumi, methylumi, Gviz, genoset, SummarizedExperiment, IRanges, GenomicRanges, VariantAnnotation, rtracklayer, GenomicFeatures, annotate, Biobase(>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods, parallel |
| System Requirements | |
| URL |
See More
| Suggests | FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | methylumi |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | methyAnalysis_1.26.0.tar.gz |
| Windows Binary | methyAnalysis_1.26.0.zip |
| Mac OS X 10.11 (El Capitan) | methyAnalysis_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/methyAnalysis |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methyAnalysis |
| Bioc Package Browser | https://code.bioconductor.org/browse/methyAnalysis/ |
| Package Short Url | https://bioconductor.org/packages/methyAnalysis/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |