DeepBlue Features

Thousand of datasets
DNA Methylation, Histone Modifications and Variants, DNaseI, Transcription Factors Binding Sites, Chromatin State Segmentation, and Gene Expression (mRNA) data from the major epigenome consortia: ENCODE, ROADMAP Epigenomic, BLUEPRINT Epigenome, and DEEP.
Operations for epigenomic data
Select, filter, summarize, transform, and download the epigenomic data. See some examples on our examples page.
Peaks and signal data experiments
DeepBlue contains the peaks (bed) and signals (wig, bedgraph) datasets. It is possible to import virtually any file that is based on genomic region into DeepBlue.
Auxiliary annotations
Genes, promoters, CpG island, transcripts, and more. You are welcome and encouraged to upload their respective annotations.
Language agnostic
The access is made via an XML-RPC protocol that is supported by all major programming languages.
Metadata consistency
Every experiment has 5 mandatory fields (genome, epigenetic mark, sample, technique, and project) that are registered with their metadata in their collections for data consistency.
Flexible metadata model
DeepBlue ensures the metadata consistency through the mandatory fields (genome, epigenetic mark, sample, technique, and project). More information about the data can be included using the extra-metadata, a key-value container, where any information about the data can be stored and searched.
Names from ontologies
DeepBlue imports the biological source names (cell lines, cell types, tissues, organs, and others) from the CL, EFO, and UBERON ontologies. The terms' synonyms and hierarchies are imported together with the terms' names.
Full text search
DeepBlue full text search is expanded to all experiments' metadata and controlled vocabularies. The samples' information, genomes, epigenetic marks, techniques, experiments, and annotations metadata are indexed and searchable by full text input.
Upload your own data
You can upload your own experimental and annotation data.
Private experimental data
You can create your own private projects, where the stored experiments there are only visible to you and invited colleagues.
Processing in ours servers
The operations are performed directly on the data server. You need only download the final result.
Reproducing analysis steps
The data operations are stored in the server and can be re-executed and shared with colleagues. DeepBlue automatically documents all steps executed during the analysis.
Web Interface
You can browse, search, and download the data included into DeepBlue using our user-friendly interface.
Anonymous access
You are not obligated to create an account. You can access DeepBlue data and its main features without having to register.