Welcome to the DKFZ UNITE organization on GitHub.
UNITE is platform for integration and analysis of different types of biomedical data.
The following data types are currently supported:
- Patient data
- Donors - general patient data including projects and studies the patient is part of
- Clinical data
- Treatments data
- Images data - metadata of images (not the images themselves)
- Images data of different types (MR)
- Radiomics features data
- Specimens data - donor specimens data and specimens hierarchy
- Specimens of differen types (Material, Line, Organoid, Xenograft)
- Molecular data
- Interventions data
- Drugs screening data
- Genome data
- Variants - SMs, CNVs, SVs
- Methylation data
- Bulk gene expressions data
- Single cell gene expression data
The core functionality of the platform is following:
- Data submission - data can be submitted in different formats via web interface or API
- Data validation - data is validated before it is stored in the database
- Data storage - data is standardized, integrated and stored in central database in structured form
- Data annotation - data is annotated using different tools (e.g. Ensembl VEP, Ensembl Database)
- Data indexing - data is indexed for fast search and retrieval
- Web interface - data can be accessed via web interface
- Cross reference search
- Dataset management tools
- Vizualization tools
- Data export tools
- Identity management
- Different identity providers (Integrated or LDAP)
- Users management - access to data is restricted to users in allow list with different permissions
- Workers management - access to data can be granted to external services (e.g. for automatic data submission or data analysis)
- Authentication/Authorization - access to data is restricted to authenticated users/workers
- Analysis
- Bulk RNA differential expression analysis (DESeq2)
- Single cell RNA dataset creation analysis.
- Donors survival estimation analysis (Kaplan-Meier).
- Differential methylation analysis (Minfi).
- Methylation principal component analysis (Minfi).
- Docker integration - all components are dockerized and can be deployed on any supported platform
- Installation - installation instructions
- Architecture - architecture of the platform and its components
- Data structure - data structure of the platform
