Features
Among the DeepBlue Features, we can highlight:
- DeepBlue contains the Methylation (WGBS, RRBS, and Infinium 450k), Histone Modifications and Variants, DNaseI, Transcription Factors Binding Sites, Chromatin State Segmetation, and gene expression (mRNA-seq) datasets from the major epigenome consortia: ENCODE, Roadmap Epigenomic (planning), DEEP (planning), and BLUEPRINT Epigenomics
- Update module that retrieves the latest epigenome datasets from the major epigenome consortia
- Access via an XML-RPC protocol that is supported by all major programming languages
- Web Interface (in development)
- User data upload facility
- Analysis operations performed directly on the data server
- Reproducibility by automatic documenting and storing of the analysis steps
- Controlled vocabulary to ensure data consistency
- Full text search command, expanded for all experiments metadata and controlled vocabularies
- BioSources data hierarchy and synonyms
- Flexible data model for storing experiments metadata
- Data Compression
- Data scalability through data distribution across several compute nodes (sharding), provided by MongoDB
- A set of operations for working with the data (see below)
Operations:
- Select epigenomic data from pre-installed datasets or datasets uploaded by the user
- Filter epigenomic data by metadata
- Filter epigenomic data by region attributes
- Find overlapping regions sets
- Group regions
- Retrieve DNA sequences
- DNA pattern matching operations
- Aggregate and summarize regions
- Count regions
- Output in BED format with desired columns