methylumi
https://bioconductor.org/packages/methylumiThis package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.
Sourced from
- Bioconductor — methylumi
Related resources
"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.
Tools to analyze & visualize Illumina Infinium methylation arrays.
Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.