Somatic copy-number alteration identification software tools | DNA methylation microarray data analysis
The 450k platform is based on similar biochemical reaction principle and technology as the Infinium SNP arrays, making it possible to use the 450k platform to detect copy number variants (CNVs) as a zero-cost byproduct of methylation studies. CN calling consists of the following principal steps: normalization of probe intensities, calculation of the Log R Ratios (LRRs), segmentation and determination of copy number status for each segment based on a chosen cutoff level or a P-value threshold.
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).
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.
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.
Enhanced copy-number variation analysis using Illumina 450k methylation arrays. conumee contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k methylation arrays.