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GenomeRunner

Annotation and enrichment of Next-Gen sequencing data

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Description

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.

GenomeRunner Web Site

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)

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  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Nice, thank you

    Posted 06/19/2013
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Additional Project Details

Intended Audience

Science/Research, End Users/Desktop

User Interface

Project is a user interface (UI) system

Programming Language

Visual Basic .NET

Registered

2011-08-22

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