MethylAid
https://bioconductor.org/packages/MethylAidA visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.
Sourced from
- Bioconductor — MethylAid
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.
Tools for quanlity control, analysis and visulization of Illumina DNA methylation array data.
Tools to analyze & visualize Illumina Infinium methylation arrays.
Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.
Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE.
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.