Software available at:
https://github.com/ChrisMaherLab/

SV-HotSpot: A tool for detection and visualization of genome hotspots targeted by recurrent structural variants  associated with gene expression.

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Eteleeb AM, Quigley DA, Zhao SG, Pham D, Yang R, Dehm SM, Luo J, Feng FY, Dang HX, Maher CA. SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression. Sci Rep. 2020 Sep 28;10(1):15890. doi: 10.1038/s41598-020-71168-7. PMID: 32985524; PMCID: PMC7522247.

INTEGRATE-Vis: A gene fusion visualization tool.

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Zhang J, Gao T, Maher CA. INTEGRATE-Vis: a tool for comprehensive gene fusion visualization. Sci Rep. 2017 Dec 19;7(1):17808. doi: 10.1038/s41598-017-18257-2. PMID: 29259323; PMCID: PMC5736641.

INTEGRATE: A tool for calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data.

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Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA. INTEGRATE: gene fusion discovery using whole genome and transcriptome data. Genome Res. 2016 Jan;26(1):108-18. doi: 10.1101/gr.186114.114. Epub 2015 Nov 10. PubMed PMID: 26556708; PubMed Central PMCID: PMC4691743.

INTEGRATE-Neo: A tool for gene fusion neoantigen discovery using next-generation sequencing data.
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Zhang J, Mardis ER, Maher CA. INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery. Bioinformatics. 2016 Oct 24. pii: btw674. [Epub ahead of print] PubMed PMID: 27797777.

ChimeraScan: A tool for discovery of chimeric transcripts in high-throughput sequencing data. 

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Iyer MK, Chinnaiyan AM, Maher CA. ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics. 2011 Oct 15;27(20):2903-4. doi: 10.1093/bioinformatics/btr467. Epub 2011 Aug 11. PubMed PMID: 21840877; PubMed Central PMCID: PMC3187648.

 

ClonEvol: A tool for inferring and visualizing clonal evolution in multiple samples. 

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Dang HX, White BS, Foltz SM, Miller CA, Luo J, Fields RC, Maher CA. ClonEvol: clonal ordering and visualization in cancer sequencing. Ann Oncol. 2017 Dec 1;28(12):3076-3082. doi: 10.1093/annonc/mdx517. PMID: 28950321; PMCID: PMC5834020.