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FusionHunter | Identifying fusion transcripts in cancer using paired-end RNA-seq

Identifies fusion transcripts from transcriptional analysis of paired-end RNA-seq. FusionHunter can accurately detect fusions that were previously confirmed by RT-PCR in a publicly available dataset. This high-throughput software tool is designed for efficient and precise detection of fusion transcripts in cancer for further functional validation in the laboratory.

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FusionHunter classification

FusionHunter specifications

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GNU General Public License version 2.0

FusionHunter distribution


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FusionHunter support


  • Jian Ma <>


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Department of Bioengineering, University of Illinois, Urbana, IL, USA; Institute for Genomic Biology, University of Illinois, Urbana, IL, USA; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA

Funding source(s)

National Center for Supercomputing Applications (Faculty fellowship); the Mayo-UIUC Alliance (Planning grant)

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