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Resources: External Applications

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  1. Trinity: RNA-Seq De novo Assembly Application

    24 Jul 2015 | External Applications | Contributor(s): Mervi Heiskanen

    Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied...

  2. CERR: A Computational Environment for Radiotherapy Research

    28 Oct 2014 | External Applications | Contributor(s): Joseph Deasy

    CERR (pronounced 'sir') is a software platform for developing and sharing research results in radiation therapy treatment planning.CERR is written in the widely-used Matlab language (version 7.0 or later), allowing for low-cost development of visualization and analysis tools.CERR will...

  3. DWIConvert

    04 Mar 2015 | External Applications | Contributor(s): Vince Magnotta, Hans Johnson, Joy Matsui, Kent Williams, Mark Scully, Xiaodong Tao

    Converts diffusion weighted MR images in dicom series into Nrrd format for analysis in Slicer. This program has been tested on only a limited subset of DTI dicom formats available from Siemens, GE, and Phillips scanners. Work in progress to support dicom multi-frame data. The program parses dicom...

  4. MC-GPU at Google Code

    12 Mar 2015 | External Applications | Contributor(s): Andreu Badal

    Link to MC-GPU at Google Code

  5. 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...

  6. 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...

  7. cBioPortal

    29 Jan 2016 | External Applications | Contributor(s): Zhiping Gu

    The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets, The current available studies: TCGA and ICGC projects, -cell line, prostate mskcc, esophageal OR stomach , Ovarian serous, and breast cancer. Available datatype: genetic...

  8. Groups of interest at the National Institutes of Health

    21 Jun 2016 | External Applications | Contributor(s): Chanelle Case Borden

    Network of African-American Fellows at the NIH (NAAF): The mission of this group is to create an environment of support for African American scientists during their tenure at NIH. To become a member of the network, please Join the NIH-NAAF listserv.  To learn more about NAAF, please visit...

  9. Human Disease Ontology

    21 Sep 2016 | External Applications | Contributor(s): Lynn Schriml

    The Disease Ontology has been developed as a standardized ontology for human disease, since 2003, with the purpose of providing the biomedical community with manual curated, consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related...

  10. CBioPortal

    15 Feb 2017 | External Applications | Contributor(s): Schultz

    This is a link to CBioPortal