lumi
https://bioconductor.org/packages/lumiThe lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.
Sourced from
- Bioconductor — lumi
Related resources
QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.
Tools for quanlity control, analysis and visulization of Illumina DNA methylation array data.
De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.
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.