Note: This version requires additional SQLite database files. Contact the developers to obtain them.
Use http://www.integrativegenomics.org/ for the latest data and analyses.
GenomeRunner is a tool for automating genome exploration. It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser.
Input - any genome-wide data data in .bed format (tab-delimited text file with chrom, chromStart, chromEnd).
Annotation analysis output - detailed annotation of each genomic region in input data. Used to prioritize individual genomic regions by the total number of epigenomic features they co-localize with.
Enrichment analysis output - p-values of statistically significant co-localizations of input genome-wide data with genome annotation features selected for the analysis. Used to prioritize epigenomic features associated with user data.
- Analysis of genomic regions (ChIP-seq, RNA-seq, DNA methylation, SNPs/CNVs etc.)
- ENCODE data
- Annotation and Enrichment analyses
- BED file format (chrom, chromStart, chromEnd)
- Video overview (http://youtu.be/v9p9FClrqXU)
Nice, thank you