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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("methyAnalysis")
In most cases, you don't need to download the package archive at all.
methyAnalysis
DNA methylation data analysis and visualization
Bioconductor version: 3.0
The methyAnalysis package aims for the DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focus on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data.
Author: Pan Du, Richard Bourgon
Maintainer: Pan Du <dupan.mail at gmail.com>
Citation (from within R,
enter citation("methyAnalysis")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("methyAnalysis")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("methyAnalysis")
| R Script | An Introduction to the methyAnalysis package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DNAMethylation, Microarray, Software, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), grid, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, Biobase(>= 2.5.5), org.Hs.eg.db |
| Imports | lumi, methylumi, Gviz, genoset, GenomicRanges, IRanges, rtracklayer, GenomicFeatures, annotate, Biobase(>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods, parallel |
| LinkingTo | |
| Suggests | FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | methylumi |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | methyAnalysis_1.8.0.tar.gz |
| Windows Binary | methyAnalysis_1.8.0.zip |
| Mac OS X 10.6 (Snow Leopard) | methyAnalysis_1.8.0.tgz |
| Mac OS X 10.9 (Mavericks) | methyAnalysis_1.8.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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