Serves for importation, quality control (QC), analysis, and visualization of methylation data generated using Sequenom's MassArray platform. MassArray is a program able to perform detailed amplicon prediction for optimal assay design. It can also inform researchers about quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Additionally, it can flag potentially confounded data from specific CG sites by using automatic single nucleotide polymorphism (SNP)-detection.
Permits rigorous statistical investigation of genomic data. Genomic HyperBrowser can serve for a range of genomic investigations that query characteristics of individual tracks or relations between pairs of tracks along the genome. It is able to differentiate 15 types of tracks at the generic level. This tool furnishes programs for customizing data into forms that eases subsequent analyses.
Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.
Generates cell differentiation associated with heatmaps highlighting important candidate cis-regulatory elements (ccRE) clusters for lineage specific epigenetic events and their associated functions. Snapshot is based on a model-free clustering approach that doesn’t need a predetermined number of clusters which can detect all abundant ccRE clusters. It offers individual index-set data visualization that enables users to combine ccRE clusters with annotations.
Allows user-friendly data exploration, visualization and interpretation of allelic imbalance. MEA furnishes integrated allele-specific analysis of DNA methylation, histone modification and expression data. This software automates diploid pseudo genome reconstruction, allele-specific read detection and haplotype-resolved. It can be used without needing extensive bioinformatic expertise and be installed into a Docker container.