Epiviz File Server

Epiviz File Server provides indexed-file querying and on-the-fly transformations of genomic data to enable efficient access and remote interrogation of large-scale datasets such as The Cancer Genome Atlas, the Encyclopedia of DNA Elements (ENCODE), Bioconductor's AnnotationHub, and ExperimentHub.

Key Features:

• In situ Data Query System: Performs direct queries against local and remotely hosted indexed genomic files to avoid full-file downloads.
• Decoupled Data Retrieval and Transformation: Separates data retrieval from transformation via an abstract interface so computations are defined independent of file location, format, or structure.
• Integration with Existing Workflows: Integrates with Galaxy workflows for incorporation into bioinformatics pipelines.
• Custom Genome Browser Creation: Supports creation of custom genome browsers and integration with the Epiviz visualization platform using datasets such as the Epigenome Roadmap.

Scientific Applications:

• Targeted exploratory analysis: Enables retrieval and transformation of subsets from large flat or indexed files for rapid exploratory analyses of datasets such as TCGA and ENCODE.
• Pipeline integration: Embeds within Galaxy-based pipelines for large-scale processing and analysis of genomic data.
• Visualization for genetics and epigenetics: Facilitates construction of tailored genome browser views for visualization and interpretation of genetic and epigenetic data (for example, Epigenome Roadmap datasets) via Epiviz.

Methodology:

A Python library that implements an abstract interface to query indexed local and remote flat files and to decouple data retrieval from transformation.