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metafusion-clinical

https://github.com/ccmbioinfo/metafusion-clinical

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (1.7%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: ccmbioinfo
  • License: bsd-3-clause-clear
  • Language: Perl
  • Default Branch: master
  • Size: 43.4 MB
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 1
  • Open Issues: 2
  • Releases: 0
Created almost 5 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.md

MetaFusion-Clinical

MetaFusion Clinical implementation wiki is here: https://github.com/ccmbioinfo/MetaFusion-Clinical/wiki

Clinical manuscript published in the Journal of Molecular Diagnostics: https://www.jmdjournal.org/article/S1525-1578(23)00211-8/fulltext


Initial implementation

Initial implementation of MetaFusion can be found here: https://github.com/ccmbioinfo/MetaFusion

Initial methods manuscript published in Bioinformatics: https://academic.oup.com/bioinformatics/article/37/19/3144/6263829

Owner

  • Name: Centre for Computational Medicine at SickKids
  • Login: ccmbioinfo
  • Kind: organization
  • Location: Canada

The Centre for Computational Medicine (CCM) is a Core Facility within the SickKids Research Institute. Email: ccm dot contact at sickkids dot ca

Citation (CITATION.cff) 

cff-version: 1.2.0
title: MetaFusion-Clinical
message: >-
  A high-confidence metacaller for filtering and
  prioritizing RNA-seq gene fusion candidates.
type: software
authors:
  - family-names: Apostolides
    given-names: Michael
    affiliation: >-
      Centre for Computational Medicine, The Hospital for
      Sick Children, Toronto, ON, Canada
  - family-names: Jiang
    given-names: Yue
    affiliation: >-
      Centre for Computational Medicine, The Hospital for
      Sick Children, Toronto, ON, Canada
  - family-names: Li
    given-names: Michael
    affiliation: >-
      Centre for Computational Medicine, The Hospital for
      Sick Children, Toronto, ON, Canada
  - family-names: Siddaway
    given-names: Robert
    affiliation: >-
      Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada

      The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
      
      Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
    email: robert.siddaway@sickkids.ca
repository-code: 'https://github.com/ccmbioinfo/MetaFusion-Clinical'
license: BSD-3-Clause-Clear
preferred-citation:
  title: >-
    Clinical Implementation of MetaFusion for Accurate Cancer-Driving 
    Fusion Detection from RNA Sequencing
  type: article
  journal: Journal of Molecular Diagnostics
  volume: "TBA"
  issue: "TBA"
  year: 2023
  doi: 10.1016/j.jmoldx.2023.09.002
  authors:
    - family-names: Apostolides
      given-names: Michael
      affiliation: >-
        Centre for Computational Medicine, The Hospital for Sick Children,
        Toronto, ON, Canada
    - family-names: Li
      given-names: Michael
      affiliation: >-
        Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada
    - family-names: Arnoldo
      given-names: Anthony
      affiliation: >-
        Centre for Computational Medicine, The Hospital for Sick Children,
        Toronto, ON, Canada
    - family-names: Ku
      given-names: Michelle
      affiliation: >-
        The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital
        for Sick Children, Toronto, ON, Canada

        Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
    - family-names: Husić
      given-names: Mia
      affiliation: >-
        Centre for Computational Medicine, Hospital for Sick Children, 
        Toronto, Ontario, Canada
    - family-names: Ramani
      given-names: Arun K.
      affiliation: >-
        Centre for Computational Medicine, The Hospital For Sick Children,
        Toronto, ON, Canada
    - family-names: Brudno
      given-names: Michael
      affiliation: >-
        Centre for Computational Medicine, The Hospital For Sick Children,
        Toronto, ON, Canada
        
        Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
        
        University Health Network, Toronto, Ontario, Canada
    - family-names: Turinsky
      given-names: Andrei L.
      affiliation: >-
        Centre for Computational Medicine, The Hospital For Sick Children,
        Toronto, ON, Canada
    - family-names: Hawkins
      given-names: Cynthia
      affiliation: >-
        Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada
        
        The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, 
        Toronto, Ontario, Canada

        Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
        
        Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
      email: cynthia.hawkins@sickkids.ca
    - family-names: Siddaway
      given-names: Robert
      affiliation: >-
        Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada

        The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
        
        Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
      email: robert.siddaway@sickkids.ca
references:
  - title: "MetaFusion-Clinical reference files"
    type: data
    doi: "10.6084/m9.figshare.24239689.v1"
    authors:
      - family-names: Apostolides
        given-names: Michael
        affiliation: >-
          Centre for Computational Medicine, The Hospital for Sick Children,
          Toronto, ON, Canada
  - title: "MetaFusion.clinical.simg"
    type: software
    doi: "10.6084/m9.figshare.14454342.v1"
    authors:
      - family-names: Apostolides
        given-names: Michael
        affiliation: >-
          Centre for Computational Medicine, The Hospital for Sick Children,
          Toronto, ON, Canada
  - title: >-
      MetaFusion: A high-confidence metacaller for filtering and prioritizing
      RNA-seq gene fusion candidates
    type: article
    journal: Bioinformatics
    volume: 37
    issue: 19
    year: 2021
    doi: 10.1093/bioinformatics/btab249
    authors:
      - family-names: Apostolides
        given-names: Michael
        affiliation: >-
          Centre for Computational Medicine, The Hospital for Sick Children,
          Toronto, ON, Canada
      - family-names: Jiang
        given-names: Yue
        affiliation: >-
          Centre for Computational Medicine, The Hospital for Sick Children,
          Toronto, ON, Canada
      - family-names: Husić
        given-names: Mia
        affiliation: >-
          Centre for Computational Medicine, The Hospital for Sick Children,
          Toronto, ON, Canada
      - family-names: Siddaway
        given-names: Robert
        affiliation: >-
          The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital
          for Sick Children, Toronto, ON, Canada
      - family-names: Hawkins
        given-names: Cynthia
        affiliation: >-
          The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital
          for Sick Children, Toronto, ON, Canada
      - family-names: Turinsky
        given-names: Andrei L.
        affiliation: >-
          Centre for Computational Medicine, The Hospital For Sick Children,
          Toronto, ON, Canada
      - family-names: Brudno
        given-names: Michael
        affiliation: >-
          Centre for Computational Medicine, The Hospital For Sick Children,
          Toronto, ON, Canada
      - family-names: Ramani
        given-names: Arun K.
        affiliation: >-
          Centre for Computational Medicine, The Hospital For Sick Children,
          Toronto, ON, Canada

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