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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).

CopyNumber450kCancer

Provides a novel functionality to correct the center in segmentation data obtained from copy number calling tools such as CopyNumber450k and ChAMP. CopyNumber450kCancer implements the maximum density peak estimation (MDPE) method together with interactive reviewing to efficiently correct the baseline in cancer samples. The main advantages for CopyNumber450kCancer are: fast auto-correction (few seconds per sample), high accuracy rate, in-sample correction, no input parameters needed, low computer resources required, and adaptable to 450k-similar technologies.

cnAnalysis450k

Realizes the normalization, segmentation and aggregation of Illumina methylation array copy number (CN) data (450k + EPIC). CnAnalysis450k allows to directly compare any preprocessed CN data. It provides its own CN alteration detection methodology: segments are identified through detection of changes in variance of CN data and are subsequently filtered for significance. The gain/loss definition can be identified automatically through analysis of the resulting ∆CN distributions of all analyzed samples.