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ChAMP
Allows Illumina HumanMethylation BeadChip analysis. ChAMP is an integrated analysis pipeline including functions for (i) filtering low quality probes, adjustment for Infinium I and Infinium II probe design, (ii) batch effect correction, detecting differentially methylated positions (DMPs), (iii) finding differentially methylated regions (DMRs) and (iv) detection of copy number aberrations. The software also allows detection of differentially methylated genomic blocks (DMB) and Gene Set Enrichment Analysis (GSEA).
Methylumi
A package that 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.
minfi
A suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. minfi provides methods for preprocessing, quality assessment and detection of differentially methylated regions from the kilobase to the megabase scale. Several preprocessing algorithms are available and the infrastructure provides a convenient way for developers to easily implement their techniques as Bioconductor tools. By making SNP annotation available, users can choose to be cautious about probes that may behave unexpectedly due to the inclusion of a SNP in the probe sequence. minfi is unique in that it provides both bump hunting and block finding capabilities, and the assessment of statistical significance for the identified regions. Finally, because the package is implemented in Bioconductor, it gives users access to the countless analysis and visualization tools available in R.
ADMIRE / Analysis of DNA methylation in genomic regions
Allows to analyze and visualize differential methylation in genomic regions. ADMIRE is a semi-automatic pipeline that features five different normalization methods and performs two one-sided two-sample rank tests (Mann–Whitney U tests). The software features arbitrary experimental settings, quality control, automatic filtering, normalization, multiple testing, differential analyses on arbitrary genomic regions. It additionally implements a gene set enrichment procedure.
GenomeStudio
Allows visualization and analysis of data generated on Illumina array platforms. GenomeStudio is a data analysis tool that provides three modules: (1) Genotyping Module for the analysis of single nucleotide polymorphism (SNPs) and copy number variations (CNVs) data and detection of sample outliers, (2) Gene Expression Module for the detection of cytosine methylation at single-base resolution and identification of methylation signatures across the entire genome, and (3) Polyploid Genotyping Module for the analysis of polyploid organism genotyping data.
EMAAS / Extensible Micro Array Analysis System
Obsolete
Consists of an application providing access resources for microarray data storage and analysis. The EMAAS infrastructure supports: (1) data transfer between specialized sites and data repositories; (2) single point access using a bespoke portal to a range of tools and packages for microarray analysis; (3) the ability to access online live expertise in data analysis from local support services for researchers; or (4) storage of raw data, analysis steps and analyzed data in an underlying relational database.
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