FILER

FILER provides harmonized access and scalable, indexing-based genomic querying of large collections of functional genomics and annotation datasets to support integration and analysis across tissues, assays, and genome builds.

Key Features:

• Comprehensive Data Collection: Integrates over 50,000 harmonized functional genomic and annotation datasets from more than 20 data sources, spanning over 1,100 biological conditions, tissues, and cell types and more than 20 experimental assays.
• Genomic Querying Interface: Implements a scalable, indexing-based genomic querying interface that supports GRCh37/hg19 and GRCh38/hg38 and encompasses over 17 billion genomic records.
• Experimental Data Annotation: Supports analysis and annotation of experimental datasets against FILER reference datasets for comparison and integration.
• Performance and Scalability: Demonstrates sub-linear scalability with respect to query size and can handle queries involving up to 1000× more genomic intervals with only a modest increase in running time.

Scientific Applications:

• High-throughput genomic and genetic analyses: Links and summarizes results across diverse data sources and types to support large-scale genomic and genetic analytical workflows.
• Integrative functional genomics: Enables integration of heterogeneous datasets across tissues, cell types, and experimental assays for functional genomics research.

Methodology:

Harmonizes datasets from multiple sources through dataset standardization and employs an indexing-based querying system for efficient genomic searches.