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  1. Open source diffusion MRI technology for brain cancer research

    07 Oct 2015 | Contributor(s): Lauren O\'Donnell

    Using measurements of water diffusion, dMRI can give unique insights into the microstructure and cellular orientation of tissues. There is a growing awareness in the neurosurgery community that diffusion models must move beyond the current clinical standard of the diffusion tensor for better...

  2. ITCR Monthly Teleconference September 4, 2015

    07 Oct 2015 | Contributor(s): Juli Klemm

     

  3. Brain Cancer Imaging Analytics

    02 Oct 2015 | Presentations | Contributor(s): Christos Davatzikos

    The transition of oncologic imaging from its “industrial era” to it is “information era” demands analytical methods that 1) extract information from this data that is clinically and biologically relevant; 2) integrate imaging, clinical, and genomic data via rigorous...

  4. "Show me the data!" Practical solutions to interactive visual analysis for big data.

    18 Sep 2015 | Presentations | Contributor(s): Samuel Payne

    Nano WG September 10, 2015.Intuitive data visualization is critical for biomedical data analysis; especially essential is the ability for non-computational scientists to productively browse the data and apply their domain knowledge.  We present Active Data Biology, a web-based visual...

  5. Trinity: RNA-Seq De novo Assembly Application

    30 Jun 2015 | External Applications | Contributor(s): Grabherr MG, Brian Haas, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Di Palma F, Birren BW, Nusbaum C, Lindblad-toh K, Friedman N, Regev A

     Quick Guide for the ImpatientTrinity assembles transcript sequences from Illumina RNA-Seq data.Download Trinity here.Build Trinity by typing make : ; in the base installation directory.Assemble RNA-Seq data like so:Trinity --seqType fq --left reads_1.fq --right reads_2.fq...

  6. CRAVAT - Cancer-Related Analysis of Variants Toolkit

    23 Jun 2015 | External Applications | Contributor(s): Rachel Karchin, Michael C Ryan

    cravat is a bioinformatics pipeline : ; that performs high-throughput cancer-related analysis of variants. it : ; utilizes three applications: CHASM (Cancer-Specific Analysis of Somatic Mutations), VEST and SVN-Get. More information on these tools is available at CHASM Software.Release...

  7. Tools for Creation of Integrated Data Repository for Cancer Research

    16 Jun 2015 | Presentations | Contributor(s): Guoqian Jiang

    Admin Supplement Proposal Parent Projects: DeepPhe (PIs: Savova and Jacobson) caCDE-QA (PI: Jiang)

  8. A Semantic Web-based Quality Assurance Tool for Cancer Study Common Data Elements

    16 Jun 2015 | Presentations | Contributor(s): Guoqian Jiang

    A poster presentation from the caCDE-QA project (PI: Jiang)  

  9. Notes from the ITCR Annual Meeting May 27-28, 2015

    10 Jun 2015 | Downloads | Contributor(s): Ishwar Chandramouliswaran, Juli Klemm

    Notes from the ITCR Annual Meeting May 27-28, 2015

  10. Introduction to the Trinity Cancer Transcriptome Analysis Toolkit

    05 Feb 2015 | Teaching Materials | Contributor(s): Brian Haas, Aviv Regev, Bill Barnett

    This short video provides an overview of our ITCR-funded effort to leverage RNA-Seq and de novo transcriptome assembly to assist researchers in studying cancer transcriptomes.  Visit our NCGAS Trinity/Galaxy portal to access these compute...

  11. CRAVAT Introduction Video - Cancer Related Analysis of Variants

    03 Dec 2014 | Teaching Materials | Contributor(s): Michael C Ryan

    This video provides a brief overview of the CRAVAT web service(http://www.cravat.us/).  CRAVAT provides annotation and analysis of cancer mutations. CRAVAT is free, very easy to use, and can handle large volumes of mutations.[[Youtube(xovmIy11Bcs)]]Please switch to 1080 resolution and watch...

  12. Analysis, integration and visualization of DNA methylation sequencing data

    07 Nov 2014 | Presentations | Contributor(s): Maureen Sartor

    Integrative epigenomic/genomic profiling and biomarker discovery of HPV+ and HPV- squamous cancers.

  13. Summarization of Big Data

    07 Nov 2014 | Presentations | Contributor(s): Jeffrey A. Blimes

    All about assay selection...

  14. Summarization of Big Data

    07 Nov 2014 | Presentations | Contributor(s): Jeffrey A. Blimes

    All about assay selection...

  15. Biomedical Evidence Graph

    03 Oct 2014 | Presentations | Contributor(s): Josh Stuart

  16. Tools to Analyze Morphology and Spatially Mapped Molecular Data

    03 Oct 2014 | Presentations | Contributor(s): Joel Saltz

  17. ITCR PI Meeting June 2014 Presentations

    23 Jun 2014 | Series

    Informatics Technology for Cancer Research (ITCR) Initiative held its Annual PI Meeting on June 12-13, 2014 in Rockville, MD. This series contains the presentations given at the meeting.

  18. Cloud Supercomputer Aided Diagnostic Imaging Decision Support System

    18 Jun 2014 | Presentations | Contributor(s): Hiro Yoshida

    ITCR PI meeting presentation on project status.

  19. Quantitative Image Informatics for Cancer Research (QIICR)

    04 Apr 2014 | Presentations | Contributor(s): Andrey Fedorov, Ron Kikinis

  20. Informatics to enable Routine Personalized Cancer Therapy (IPCT)

    18 Feb 2014 | Presentations | Contributor(s): Elmer V. Bernstam, Funda Meric-Bernstam