genomerunner

We have hosted the application genomerunner in order to run this application in our online workstations with Wine or directly.

Quick description about genomerunner:

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.

Features:

• 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)

Audience: Science/Research, End Users/Desktop.
User interface: Project is a user interface (UI) system.
Programming Language: Visual Basic .NET.
Database Environment: SQL-based.

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