Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

Nature Methods
Kun QuJill P Mesirov

Abstract

Complex biomedical analyses require the use of multiple software tools in concert and remain challenging for much of the biomedical research community. We introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate integrative analysis by non-programmers, it offers a growing set of 'recipes', short workflows to guide investigators through high-utility analysis tasks.

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Citations

Oct 30, 2016·Nucleic Acids Research·Ricardo LebrónJosé L Oliver
Feb 24, 2017·Molecular Diagnosis & Therapy·Thomas Milan, Brian T Wilhelm
May 26, 2017·PLoS Computational Biology·Björn A GrüningAnton Nekrutenko
Oct 18, 2018·Bioinformatics·Shayoni RaySylvain V Costes
Dec 28, 2017·Nature Reviews. Genetics·Marcin Cieślik, Arul M Chinnaiyan
Jan 24, 2020·PLoS Biology·Charles BlattiSaurabh Sinha
Oct 3, 2018·F1000Research·Kidane M TekleInge Jonassen
Jan 22, 2020·Nature Methods·Daniel BlankenbergNate Coraor
May 24, 2018·Nucleic Acids Research·Enis AfganDaniel Blankenberg
Jun 15, 2019·Bioinformatics·Vahid JaliliJeremy Goecks
Nov 8, 2018·BMC Bioinformatics·Erno LindforsMaria Suarez-Diez
Jul 17, 2020·Computational and Structural Biotechnology Journal·George MinadakisGeorge M Spyrou
Mar 7, 2021·Briefings in Functional Genomics·Dariusz R AugustynDariusz Mrozek
Jun 23, 2021·Nucleic Acids Research·David KnuppPedro Miura
May 8, 2021·Bioinformatics·Justyna D Kryś, Dominik Gront
Sep 11, 2021·Briefings in Bioinformatics·Piotr GrzesikDariusz Mrozek

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Software Mentioned

Dropbox
Genomica
GenomeSpace Recipe
GenomeSpace suite
UCSC Table Browser
Integrative Genomics Viewer ( IGV )
Cytoscape
geWorkbench
cBioPortal
GenomeSpace

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