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GobyWeb specifications

Information


Unique identifier OMICS_00601
Name GobyWeb
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Fabien Campagne <>

Publication for GobyWeb

GobyWeb in publications

 (7)
PMCID: 5556007
PMID: 28808241
DOI: 10.1038/s41598-017-07922-1

[…] from fastq sanger format to compact-reads format and then align with star (default parameters) to the mouse reference genome (mgc37/mm9). data alignment and analysis were performed using the gobyweb interface using ensembl version 55. differential expression was computed using the edger package from bioconductor. data were also examined visually in the integrative genomic viewer […]

PMCID: 5118799
PMID: 27874028
DOI: 10.1038/srep37366

[…] library preparation kit, following the manufacturers’ recommended protocol. samples were multiplexed 6 per lane and sequenced on an illumina hiseq 4000 instrument., reads were uploaded to the gobyweb system and aligned to the 1000 genome human reference sequence with the star aligner. ensembl annotations for transcripts were obtained from biomart and ensembl automatically using gobyweb. […]

PMCID: 5042552
PMID: 27684477
DOI: 10.1371/journal.pcbi.1005088

[…] initial evidence that differences across dna that code for a large number of proteins can have a combined impact on graft function., the genotype input file(s) necessary to reproduce these results (gobyweb tags: jeohqur (2.3gb), yoolwxh (83mb)) cannot be distributed through dbgap (http://www.ncbi.nlm.nih.gov/gap), or an equivalent archive, because the consent form signed by the ctot-04 […]

PMCID: 4382166
PMID: 25830305
DOI: 10.1371/journal.pone.0120649

[…] for testing novel therapies that target altered tumor metabolism to inhibit ccrcc., we thank sagit goldenberg for assistance in obtaining human ccrcc tissue samples, dr. campagne for help with gobyweb, dr. tuo zhang for help with the rnaseq data, and members of the gudas, nanus, and gross laboratories […]

PMCID: 4349052
PMID: 25755929
DOI: 10.7717/peerj.800

[…] readers are refered to and for an introduction to language workbench (lw) technology. we previously discussed the advantages of lw technology in bioinformatics in the context of the development of gobyweb plugin scripts (). in this new study, we investigated whether lw technology—specifically the mps language workbench (see http://www.jetbrains.com/mps/ and )—could be used to model […]


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GobyWeb institution(s)
The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, The Weill Cornell Medical College, New York, NY, USA; Department of Physiology and Biophysics, The Weill Cornell Medical College, New York, NY, USA
GobyWeb funding source(s)
This work was supported by grant UL1 RR024996 (NIH/NCRR) of the Clinical and Translation Science Center at Weill Cornell Medical College, by grant LLS 6304-11 from the Lymphoma and Leukemia Society Translational Research Program, and by R01 MH086883 (NIH/NIMH). Support was also provided by the Tri-Institutional Training Program in Computational Biology and Medicine.

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