RNAbrowse protocols

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RNAbrowse specifications

Information


Unique identifier OMICS_04047
Name RNAbrowse
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.4
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jérôme Mariette <>

Information


Unique identifier OMICS_04047
Name RNAbrowse
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.4
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jérôme Mariette <>

Publication for RNAbrowse

RNAbrowse in pipeline

2018
PMCID: 5936029
PMID: 29728057
DOI: 10.1186/s12864-018-4668-z

[…] indels). the resulting bam files were processed with gatk (−glm both parameter, version v3.0–0-g6bad1c6) following the best practices found on the gatk website []. all the results were uploaded in a rnabrowse instance [] and can be accessed from the web at http://ngspipelines.toulouse.inra.fr:9007/., the table of raw mapped read counts per replicate (each of which is made up of 10 pooled mites) […]


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RNAbrowse in publications

 (2)
PMCID: 5936029
PMID: 29728057
DOI: 10.1186/s12864-018-4668-z

[…] indels). the resulting bam files were processed with gatk (−glm both parameter, version v3.0–0-g6bad1c6) following the best practices found on the gatk website []. all the results were uploaded in a rnabrowse instance [] and can be accessed from the web at http://ngspipelines.toulouse.inra.fr:9007/., the table of raw mapped read counts per replicate (each of which is made up of 10 pooled mites) […]

PMCID: 4707302
PMID: 26793234
DOI: 10.3389/fgene.2015.00361

[…] disk image (available on github), which contains all the required dependencies to run the software using a virtual machine. alternatively, afterparty is also available through a public server., rnabrowse is an alternative package with a web interface that can be used to store and visualize de novo transcriptome data (mariette et al., ). it is based on the biomart (smedley et al., ) software […]


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RNAbrowse institution(s)
Plate-forme bio-informatique Genotoul/Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France; Plate-forme SIGENAE/Génétique Cellulaire, INRA, Castanet-Tolosan, France

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