ifb services cloud

Tools deployed by IFB platforms

  • Absynte

    3 Associated keyword(s)
    • Sequence analysis
    • Interfaces, web portals
    • Genome comparison

    web server + web service, http://archaea.u-psud.fr/absynte Gratuit pour u-psud.

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  • ACNUC

    3 Associated keyword(s)
    • Information and communication technology developments
    • Data
    • Databases and information systems

    Freely downloadable software licensed under the GNU General Public License (http://doua.prabi.fr/databases/acnuc) or on-line access through a web interafce (http://doua.prabi.fr/search/query_fam).

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  • ActivCollector

    1 Associated keyword(s)
    • No relevant terms in the list above

    Gratuit

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  • ADE-4

    4 Associated keyword(s)
    • Biostatistics
    • Multivariate analysis
    • Ecology
    • Microbial ecology

    Freely available for download from any CRAN mirror.

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  • AGMIAL

    3 Associated keyword(s)
    • Genomics (DNA-seq)
    • Genome analysis
    • Structural and functional genome annotation

    Le logiciel peut être téléchargé gratuitement sur le site http://genome.jouy.inra.fr/agmial. Il est également possible de demander l’installation d’une instance d’AGMIAL sur les machines de la plate-forme MIGALE.

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  • ARNold

    3 Associated keyword(s)
    • Sequence annotation
    • Sequence motif discovery
    • Structure analysis, homologous and structural motifs discovery

    web server

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  • Askomics

    5 Associated keyword(s)
    • NGS data analysis
    • Integration of heterogeneous data
    • Knowledge representation
    • Ontologies
    • Semantic Web

    Free

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  • Aureme

    4 Associated keyword(s)
    • Integration of heterogeneous data
    • System biology
    • Metabolic network modelling
    • Metabolic network analysis

    Free

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  • Autograph

    4 Associated keyword(s)
    • Sequence analysis
    • Homology/Orthology prediction
    • Comparative genomics
    • Genome comparison

    Free access.

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  • BCSearch

    2 Associated keyword(s)
    • Structural bioinformatics
    • Structure analysis, homologous and structural motifs discovery

    Online free access

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  • BioMAJ

    2 Associated keyword(s)
    • Data
    • Data management and transfer

    Téléchargement libre : https://github.com/genouest/biomaj

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  • BioMAJ2Galaxy

    2 Associated keyword(s)
    • Data management and transfer
    • Databases and information systems
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  • BioNJ

    3 Associated keyword(s)
    • Evolution and phylogeny
    • Molecular evolution
    • Genes and genomes

    Gratuit via le site web de la plateforme.

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  • BioShaDock

    6 Associated keyword(s)
    • Information and communication technology developments
    • Tools
    • Tool integration
    • Computing environments
    • Cluster
    • Cloud
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  • Cadbiom

    3 Associated keyword(s)
    • System biology
    • Regulatory network modelling
    • System modelling

    Free

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  • Caspo

    3 Associated keyword(s)
    • System biology
    • System modelling
    • Dynamic systems

    Free

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  • CesGO

    6 Associated keyword(s)
    • Information and communication technology developments
    • Tool integration
    • Interfaces, web portals
    • Data integration
    • Data management and transfer
    • Databases and information systems
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  • Clust&See

    3 Associated keyword(s)
    • System biology
    • Complex biological systems functions
    • Multi-layer analysis and modelling

    Libre sur http://tagc.univ-mrs.fr/tagc/index.php/clustnsee et sur l'App store.

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  • CompPhy

    5 Associated keyword(s)
    • Evolution and phylogeny
    • Molecular evolution
    • Genes and genomes
    • Phylogenomics
    • Supertrees et reconciliations

    Gratuit via le site web de la plateforme.

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  • CRAC

    4 Associated keyword(s)
    • NGS data analysis
    • Transcriptomics (RNA-seq)
    • Differential gene expression analysis
    • Transcripts and transcript variants analysis

    Gratuit via le site de la plateforme.

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  • CRISPRFinder

    2 Associated keyword(s)
    • Sequence annotation
    • Sequence motif discovery

    web sever

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  • e-BGO

    2 Associated keyword(s)
    • Interfaces, web portals
    • Databases and information systems

    Accès public.

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  • ERPIN

    4 Associated keyword(s)
    • Sequence algorithmics
    • Sequence annotation
    • Sequence motif discovery
    • Structure analysis, homologous and structural motifs discovery
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  • ESPript/ENDscript

    5 Associated keyword(s)
    • Sequence analysis
    • (multiple) Sequence Alignment
    • Sequence motif discovery
    • Structural bioinformatics
    • Structure analysis, homologous and structural motifs discovery

    http://espript.ibcp.fr et http://endscript.ibcp.fr

    Le serveur ESPript/ENDscript est accessible gratuitement, via Internet et sans enregistrement, à la communauté scientifique pour un usage académique.

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  • FastME

    3 Associated keyword(s)
    • Evolution and phylogeny
    • Molecular evolution
    • Genes and genomes

    Gratuit via le site web de la plateforme.

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  • FITBAR

    3 Associated keyword(s)
    • Sequence analysis
    • Sequence annotation
    • Sequence motif discovery

    Web server

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  • fpocket

    2 Associated keyword(s)
    • Structural bioinformatics
    • Structural property prediction

    Online free access.

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  • Frog2

    2 Associated keyword(s)
    • Structural bioinformatics
    • Structural property prediction

    Online free access

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  • GalaxEast

    1 Associated keyword(s)
    • NGS data analysis

    Open access for the French academic research community.
    Access facilitated via rapid connexions (eg : Osiris, Renater)

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  • Galaxy (piloté par Sigenae)

    5 Associated keyword(s)
    • NGS data analysis
    • Genomics (DNA-seq)
    • Transcriptomics (RNA-seq)
    • Variant calling
    • Metagenomics, metatranscriptomics

    Available on a web site with login and password.

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  • Galaxy server@URGI

    3 Associated keyword(s)
    • NGS data analysis
    • Sequence analysis
    • Comparative genomics

    https://urgi.versailles.inra.fr/galaxy

    Restricted access in the frame of collaborative project or URGI Service offering

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  • Galaxy-LD

    4 Associated keyword(s)
    • Machine learning
    • Knowledge extraction
    • Integration of heterogeneous data
    • Semantic Web
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  • Galaxy@BiRD

    13 Associated keyword(s)
    • NGS data analysis
    • Transcriptomics (RNA-seq)
    • Differential gene expression analysis
    • Variant calling
    • Panels (amplicons, captures)
    • Exomes
    • Whole genomes
    • Genomics: Chips
    • RNA chips
    • Expression
    • Proteomics
    • Quantitative proteomics
    • Statistical Differential Analysis

    L'accès à Galaxy nécessite la création d'un compte sur le cluster : http://www.pf-bird.univ-nantes.fr/07074276/0/fiche___pagelibre/&RH=14425...

     

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  • Galaxy@CBiB

    2 Associated keyword(s)
    • NGS data analysis
    • Sequence analysis

    Free web access, possibility of access to supplementary storage

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  • GATB

    10 Associated keyword(s)
    • NGS data analysis
    • Methodology
    • Genome and transcriptome assembly
    • Read mapping
    • Variant calling
    • Exomes
    • Whole genomes
    • Metagenomics, metatranscriptomics
    • Sequence analysis
    • Sequence algorithmics

    Freely available.

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  • Geno3D@

    4 Associated keyword(s)
    • Structural bioinformatics
    • Structure analysis, homologous and structural motifs discovery
    • Structural property prediction
    • Structure comparative and de novo modelling

    https://geno3d-prabi.ibcp.fr (depuis février 2001).

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  • GenRGenS

    3 Associated keyword(s)
    • Sequence algorithmics
    • Sequence motif discovery
    • Structure analysis, homologous and structural motifs discovery

    Jar + tar.gz download

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  • GO-Docker

    4 Associated keyword(s)
    • Information and communication technology developments
    • Computing environments
    • Cluster
    • Cloud
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  • GO2Pub

    6 Associated keyword(s)
    • Integration of heterogeneous data
    • Ontologies
    • Information and communication technology developments
    • Data
    • Data integration
    • Databases and information systems

    Accès libre

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  • Hex

    2 Associated keyword(s)
    • Structural bioinformatics
    • Structural property prediction

    Free licence for academic use

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  • HexServer

    2 Associated keyword(s)
    • Structural bioinformatics
    • Structural property prediction

    Free service: no login or registration required

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  • HHalign-Kbest

    2 Associated keyword(s)
    • Structural bioinformatics
    • Structure comparative and de novo modelling

    Online free access

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  • IntegronFinder

    2 Associated keyword(s)
    • Sequence annotation
    • Sequence motif discovery

    Integron_Finder is released under the GPLv3 license  and is available here: https://github.com/gem-pasteur/Integron_Finder

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  • InterEvDock

    2 Associated keyword(s)
    • Structural bioinformatics
    • Structure comparative and de novo modelling

    Online free access

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  • Interface web blast

    1 Associated keyword(s)
    • Sequence analysis

    Available on the web site.

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  • Interface web Emboss

    1 Associated keyword(s)
    • Sequence analysis

    Site web

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  • ISsaga

    7 Associated keyword(s)
    • Sequence analysis
    • (multiple) Sequence Alignment
    • Sequence annotation
    • Sequence motif discovery
    • Homology/Orthology prediction
    • Data curation
    • Genome comparison

    Les utilisateurs demandent un compte puis peuvent charger de façon illimitée, des projets d’annotation de génomes.

    Gratuit.

    NB : Le nombre de nouveaux comptes ouverts par an est comptabilisé dans "visites uniques" mais chaque utilisateur a un accès illimité à son compte et à ses génomes chargés.

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  • JFlow

    2 Associated keyword(s)
    • Workflows developments
    • Cluster

    The software package is available under the GNU General Public License (GPL) and can be downloaded from the mulcyber forge.

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  • Jvenn

    1 Associated keyword(s)
    • Interfaces, web portals

    The software package is available under the GNU General Public License (GPL) and can be downloaded from the mulcyber forge.

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  • Kpax

    2 Associated keyword(s)
    • Structure analysis, homologous and structural motifs discovery
    • Structure comparative and de novo modelling

    No-cost licence for academic use.

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  • leBiBI

    2 Associated keyword(s)
    • NGS data analysis
    • Metagenomics, metatranscriptomics

    Free online access.

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  • Logol

    2 Associated keyword(s)
    • Sequence analysis
    • Sequence motif discovery

    Utilisation interne.

    Accès libre.

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  • LoRDEC

    5 Associated keyword(s)
    • NGS data analysis
    • Methodology
    • Read mapping
    • Genomics (DNA-seq)
    • Transcriptomics (RNA-seq)

    Gratuit depuis le site web de la plateforme.

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  • LSD

    1 Associated keyword(s)
    • Speciation dating

    Gratuit via le site web de la plateforme.

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  • MEMHDX

    2 Associated keyword(s)
    • Biostatistics
    • Interfaces, web portals

    MEMHDX is freely available as a web tool at http://memhdx.c3bi.pasteur.fr/

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  • MICADo

    3 Associated keyword(s)
    • NGS data analysis
    • Methodology
    • Variant calling

    Public.

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  • Microscope

    33 Associated keyword(s)
    • NGS data analysis
    • Read mapping
    • Genomics (DNA-seq)
    • Genome analysis
    • Structural and functional genome annotation
    • Transcriptomics (RNA-seq)
    • Differential gene expression analysis
    • Variant calling
    • Whole genomes
    • Metagenomics, metatranscriptomics
    • Sequence analysis
    • Sequence algorithmics
    • (multiple) Sequence Alignment
    • Sequence annotation
    • Sequence motif discovery
    • Homology/Orthology prediction
    • System biology
    • Metabolic network modelling
    • Tools
    • Tool integration
    • Interoperability
    • Interfaces, web portals
    • Workflows developments
    • Data
    • Data integration
    • Data management and transfer
    • Databases and information systems
    • Computing environments
    • Cluster
    • Parallelisation
    • Comparative genomics
    • Genome comparison
    • Comparison of functional and regulatory pathways

    Accès libre aux données et à l'analyse des génomes publiques.

    Accès sécurisé aux données des génomes en cours d'analyse.

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  • Minia

    5 Associated keyword(s)
    • NGS data analysis
    • Methodology
    • Genome and transcriptome assembly
    • Sequence analysis
    • Sequence algorithmics

    Free

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  • MIX

    2 Associated keyword(s)
    • NGS data analysis
    • Methodology

    Free web access

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  • Mobyle

    9 Associated keyword(s)
    • Information and communication technology developments
    • Tools
    • Tool integration
    • Interoperability
    • Interfaces, web portals
    • Data
    • Data integration
    • Computing environments
    • Cluster

    The Mobyle framework is developped under the GPLv2 license.

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  • MPscan

    3 Associated keyword(s)
    • NGS data analysis
    • Methodology
    • Read mapping

    Gratuit via le site web de la plateforme.

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  • MSDA

    1 Associated keyword(s)
    • Proteomics

    Free Web access

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  • MTiAutoDock/MTiOpenScreen

    4 Associated keyword(s)
    • Structural bioinformatics
    • Virtual screening
    • Small chemical compounds libraries, 2D/3D, ADME/tox
    • Structure-based screening

    Online free access

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  • NG6

    2 Associated keyword(s)
    • Interfaces, web portals
    • Data management and transfer

    The NG6 code is freely available on the mulcyber forge. To ease the installation, the package and all its dependencies are also available as a virtual machine. Installing and maintaining the system would require expertise in Linux system administration.
    Available by the web site for users

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  • NGS-QC Generator

    1 Associated keyword(s)
    • NGS data analysis

    Free Web access for the academic research community. Premium access is also available on request.

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  • NPS@

    8 Associated keyword(s)
    • Sequence analysis
    • Sequence algorithmics
    • (multiple) Sequence Alignment
    • Sequence annotation
    • Sequence motif discovery
    • Homology/Orthology prediction
    • Structural bioinformatics
    • Structural property prediction

    https://npsa-prabi.ibcp.fr (depuis avril 1998).

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  • OCG

    2 Associated keyword(s)
    • Complex biological systems functions
    • Multi-layer analysis and modelling
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  • ORDO

    13 Associated keyword(s)
    • Machine learning
    • Knowledge extraction
    • Integration of heterogeneous data
    • Knowledge representation
    • Ontologies
    • Semantic Web
    • Data curation
    • Information and communication technology developments
    • Tools
    • Tool integration
    • Data
    • Data integration
    • Databases and information systems
    Downloadable and freely accessible via Orphadata.org,

    Downloadable and usable via Bioportal.

    Availability of a sparql EndPoint.

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  • OrthoInspector

    1 Associated keyword(s)
    • Sequence analysis
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  • PEP-FOLD

    2 Associated keyword(s)
    • Structural bioinformatics
    • Structure comparative and de novo modelling

    Online free access

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  • PepPSY

    3 Associated keyword(s)
    • Homology/Orthology prediction
    • Comparison of functional and regulatory pathways
    • Proteogenomics

    Accès libre

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  • PepTeam

    3 Associated keyword(s)
    • Sequence analysis
    • Sequence algorithmics
    • Sequence motif discovery

    Through CBiB Galaxy interface.

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  • phylogeny.fr

    3 Associated keyword(s)
    • Evolution and phylogeny
    • Molecular evolution
    • Genes and genomes

    Gratuit via le site web de la plateforme.

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  • PhyML

    3 Associated keyword(s)
    • Evolution and phylogeny
    • Molecular evolution
    • Genes and genomes

    Gratuit via le site web de la plateforme.

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  • PhySIC_IST

    3 Associated keyword(s)
    • Evolution and phylogeny
    • Phylogenomics
    • Supertrees et reconciliations

    Gratuit via le site web de la plateforme.

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  • PipeAlign

    1 Associated keyword(s)
    • Sequence analysis
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  • Protomata

    4 Associated keyword(s)
    • Sequence analysis
    • (multiple) Sequence Alignment
    • Sequence motif discovery
    • Homology/Orthology prediction

    Free

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  • QOD

    2 Associated keyword(s)
    • Comparative genomics
    • Genome comparison

    Gratuit via le site de la plateforme.

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  • Regulatory Sequence Analysis Tools (RSAT)

    6 Associated keyword(s)
    • Genomics (DNA-seq)
    • Chip-seq
    • Sequence algorithmics
    • Sequence motif discovery
    • Statistical tests
    • Comparison of functional and regulatory pathways

    Accès libre sous cinq modalités:

    • Interface Web RSAT (http://www.rsat.eu) et NeAt (htpp://neat.rsat.eu)
    • En ligne de commandes (suite téléchargeable localement)
    • Services Web (SOAP/WSDL)
    • Machines virtuelles accessibles à partir du cloud IFB (Web + ligne de commande + web service)
    • En développement interface Galaxy pour certains outils spécialisés dans l'analyse des données ChIP-Seq
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  • ReMap

    2 Associated keyword(s)
    • NGS data analysis
    • Data curation

    Libre à partir de http://tagc.univ-mrs.fr/remap

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  • REPET

    4 Associated keyword(s)
    • NGS data analysis
    • Sequence analysis
    • Evolution and phylogeny
    • Comparative genomics
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  • ReproGenomics Viewer

    2 Associated keyword(s)
    • Comparative genomics
    • Comparison of functional and regulatory pathways
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  • RNAbrowse nouvelle version

    6 Associated keyword(s)
    • NGS data analysis
    • Transcriptomics (RNA-seq)
    • Differential gene expression analysis
    • Transcripts and transcript variants analysis
    • Variant calling
    • Interfaces, web portals

    The software package is available under the GNU General Public License (GPL) and can be downloaded from the mulcyber forge.
    Available on web sites for users.

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  • RNAspace

    3 Associated keyword(s)
    • Analysis of gene expression regulation
    • Small and long non-coding RNAs
    • Sequence annotation

    RNAspace is an open source project. It is developed in Python. It is copyrighted with the GNU General Public License, and is free (in the GNU sense) for all to use, and is in constant development. RNAspace is hosted at Sourceforge. It is also available as a web server at rnaspace.org

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