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Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.


A package to detect genes that show different transcript abundances between two conditions putatively caused by alterations in histone modification. Epigenomix is based on a correlation measure for integrative analysis of ChIP-seq and gene transcription data measured by RNA sequencing or microarrays. We propose quantile normalization for ChIP-seq data and a Bayesian mixture approach involving a mixture of mixtures and distributions of different type (normal and exponential) to classify transcripts based on a measure for the correlation between histone modifications and gene transcription.


A web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain. Heat*seq allows users to contextualise their sequencing data with respect to vast amounts of public data in a few minutes without requiring any programming skills. Heat*seq currently contains over 12,000 experiments across diverse tissues and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualise user experiments. High quality figures and tables are produced and can be downloaded in multiple formats.