Online

A Bioconductor package for interactive quality control of DNA methylation data from Illumina 450k arrays. The package summarizes 450k experiments into small exportable R objects from which an interactive interface is launched. Reactive plots allow fast and intuitive quality control assessment of the samples. In addition, exploration of the phenotypic associations is possible through coloring and principal component analysis. Altogether, the package makes it easy to perform quality assessment of large-scale methylation datasets, such as epigenome-wide association studies or the datasets available through The Cancer Genome Atlas portal.

User report

0 user reviews

0 user reviews

No review has been posted.

shinyMethyl forum

No open topic.

shinyMethyl versioning

No versioning.

shinyMethyl classification

shinyMethyl specifications

Software type:
Package
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
R
Stability:
Stable

Publications

  • (Fortin et al., 2014) shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R. F1000Research.
    PMID: 25285208

Link to literature

Related DNA methylation array analysis tools

Most Recent Tools

methylSpectrum
Desktop

methylSpectrum

Deconvolutes of DNA methylation array data into source contributions from…

Deconvolutes of DNA methylation array data into source contributions from distinct cell types. methylSpectrum is a method for inferring changes in the distribution of white blood cells between…

DiMmeR
Desktop

DiMmeR Discovery of Multiple Differentially Methylated Regions

Guides scientists the whole way through EWAS data analysis. DiMmer offers…

Guides scientists the whole way through EWAS data analysis. DiMmer offers parallelized statistical methods for identifying DMRs in both Illumina 450K and 850K EPIC chip data and also methylated…

PyMAP
Desktop

PyMAP

A native python module for analysis of 450k methylation platform. PyMAP can be…

A native python module for analysis of 450k methylation platform. PyMAP can be easily deployed to cloud platforms that support python scripting language for large-scale methylation studies. By…

ICDMR
Desktop

ICDMR Identification of Consistently Differentially Methylated Regions

Analyzes methylation intensity data generated from tiling arrays to locate DMRs…

Analyzes methylation intensity data generated from tiling arrays to locate DMRs across a large set of samples simultaneously. ICDMR provides a way to calculate the concordance between adjacent…

Most Popular Tools

FastDMA
Desktop

FastDMA

A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which…

A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing.

16 related tools

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.