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Data integration software tools | DNA methylation microarray data analysis

Cancer development and progression is driven by a complex pattern of genomic and epigenomic perturbations. Both types of perturbations can affect gene expression levels and disease outcome. Integrative analysis of cancer genomics data may therefore improve detection of perturbed genes and prediction of disease state.

Source text:
(Switnicki et al., 2016) PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification. Bioinformatics.

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InCroMAP / Integrated analysis of Cross-platform MicroArray and Pathway data
A tool for the analysis and visualization of high-level microarray data from individual or multiple different platforms. Currently, InCroMAP supports mRNA, microRNA, DNA methylation and protein modification datasets. Several methods are offered that allow for an integrated analysis of data from those platforms. The available features of InCroMAP range from visualization of DNA methylation data over annotation of microRNA targets and integrated gene set enrichment analysis to a joint visualization of data from all platforms in the context of metabolic or signalling pathways.
COHCAP / City of Hope CpG Island Analysis Pipeline
Provides tools for analysing single-nucleotide resolution methylation data. COHCAP is a pipeline that covers most user needs for differential methylation and integration with gene expression data. The software includes quality control metrics, defining differentially methylated CpG sites, defining differentially methylated CpG islands and visualization of methylation data. It contains two different methods of CpG island analysis. COHCAP has been shown scalable for high-quality integrative analysis of cell line data as well as large heterogeneous patient samples.
Marmal-aid
A combined database and R package that allows you to investigate the methylation state of regions of interest across the genome. Marmal-aid is the largest publicly available Illumina HumanMethylation450 methylation database combining Illumina HumanMethylation450 data from a number of sources into a single location with a single common annotation format. This allows for automated extraction using the R package and inclusion into existing analysis pipelines. Marmal-aid also provides a easy to use GUI to visualise methylation data in user defined genomic regions for various reference tissues.
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