GET /api/tool/?format=api&offset=140&ordering=description
HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept

{
    "count": 207,
    "next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=160&ordering=description",
    "previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=120&ordering=description",
    "results": [
        {
            "id": 161,
            "name": "PEP-SiteFinder",
            "description": "PEP-SiteFinder is a web server tool for the blind identification of peptide binding sites on protein surfaces.",
            "homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-SiteFinder",
            "biotoolsID": "pep-sitefinder",
            "biotoolsCURIE": "biotools:pep-sitefinder",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_3534",
                "http://edamontology.org/topic_2275"
            ],
            "primary_publication": [
                "10.1093/nar/gku404"
            ],
            "operating_system": [],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Pierre Tufféry",
                    "email": "pierre.tuffery@univ-paris-diderot.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-1033-9895",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "Freeware",
            "documentation": "https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-SiteFinder",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 347,
            "citations": null,
            "annual_visits": 1482,
            "last_update": "2024-11-24T20:59:55.640056Z",
            "teams": [
                "RPBS"
            ],
            "source_repository": null
        },
        {
            "id": 208,
            "name": "MindTheGap",
            "description": "Performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome.",
            "homepage": "https://gatb.inria.fr/software/mind-the-gap/",
            "biotoolsID": "mindthegap",
            "biotoolsCURIE": "biotools:mindthegap",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [
                "GATB"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0199"
            ],
            "primary_publication": [
                "10.1093/bioinformatics/btu545"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "GenOuest",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Claire Lemaitre",
                    "email": "claire.lemaitre@inria.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "https://gatb.inria.fr/software/mind-the-gap/",
            "maturity": "Emerging",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T20:58:48.627968Z",
            "teams": [
                "GenOuest"
            ],
            "source_repository": null
        },
        {
            "id": 82,
            "name": "PhyML",
            "description": "Phylogenetic estimation software using Maximum Likelihood",
            "homepage": "https://www.atgc-montpellier.fr/phyml/",
            "biotoolsID": "phyml",
            "biotoolsCURIE": "biotools:phyml",
            "tool_type": [
                "Web application",
                "Command-line tool"
            ],
            "collection": [
                "elixir-fr-sdp-2019",
                "PhyML",
                "galaxyPasteur"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3293",
                "http://edamontology.org/topic_0091"
            ],
            "primary_publication": [
                "10.1093/sysbio/syq010"
            ],
            "operating_system": [
                "Linux",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Maintainer",
                        "Support",
                        "Developer",
                        "Primary contact"
                    ],
                    "name": "Stephane Guindon",
                    "email": "guindon@lirmm.fr",
                    "url": "http://stephaneguindon.github.io/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "LIRMM",
                    "email": null,
                    "url": "http://www.lirmm.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact",
                        "Developer",
                        "Maintainer",
                        "Support"
                    ],
                    "name": "Stephane Guindon",
                    "email": "guindon@lirmm.fr",
                    "url": "https://stephaneguindon.github.io/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "LIRMM",
                    "email": null,
                    "url": "https://www.lirmm.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                }
            ],
            "tool_licence": "GPL-2.0",
            "documentation": "https://github.com/stephaneguindon/phyml/blob/master/doc/phyml-manual.pdf",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T14:34:19.190685Z",
            "teams": [
                "ATGC"
            ],
            "source_repository": null
        },
        {
            "id": 240,
            "name": "SMS",
            "description": "Phylogenetic model selection using likelihood-based criteria. SMS stends for Smart Model Selection.",
            "homepage": "http://www.atgc-montpellier.fr/sms/",
            "biotoolsID": "PhyMLSMS",
            "biotoolsCURIE": "biotools:PhyMLSMS",
            "tool_type": [
                "Command-line tool",
                "Web application"
            ],
            "collection": [
                "PhyML"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3293",
                "http://edamontology.org/topic_0091",
                "http://edamontology.org/topic_2269"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [],
            "tool_licence": null,
            "documentation": "http://www.atgc-montpellier.fr/download/papers/sms-HowItWorks.pdf",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T20:59:18.380055Z",
            "teams": [],
            "source_repository": null
        },
        {
            "id": 19,
            "name": "PhylOPDb",
            "description": "Phylogenetic Oligonucleotide Probe Database. Provides a convivial and easy-to-use web interface to browse both regular and explorative 16S rRNA-targeted probes.",
            "homepage": "http://g2im.u-clermont1.fr/phylopdb/help.php",
            "biotoolsID": "phylopdb",
            "biotoolsCURIE": "biotools:phylopdb",
            "tool_type": [
                "Database portal",
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0632",
                "http://edamontology.org/topic_3293",
                "http://edamontology.org/topic_3518"
            ],
            "primary_publication": [],
            "operating_system": [],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": null,
                    "email": "pierre.peyret@udamail.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "http://g2im.u-clermont1.fr/phylopdb/help.php",
            "maturity": null,
            "cost": null,
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2018-12-10T12:58:58Z",
            "teams": [],
            "source_repository": null
        },
        {
            "id": 131,
            "name": "jvenn",
            "description": "Plug-in for the jQuery Javascript library. It is an integrative tool for comparing lists with Venn Diagrams.",
            "homepage": "http://bioinfo.genotoul.fr/jvenn/",
            "biotoolsID": "jvenn",
            "biotoolsCURIE": "biotools:jvenn",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0092",
                "http://edamontology.org/topic_2269"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": null,
                    "email": "support.genopole@toulouse.inra.fr",
                    "url": "http://bioinfo.genotoul.fr/jvenn/index.html",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "http://jvenn.toulouse.inra.fr/app/index.html",
            "maturity": null,
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-25T14:53:20.499445Z",
            "teams": [],
            "source_repository": null
        },
        {
            "id": 121,
            "name": "LoRDEC",
            "description": "Program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads.",
            "homepage": "http://www.atgc-montpellier.fr/lordec/",
            "biotoolsID": "lordec",
            "biotoolsCURIE": "biotools:lordec",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [
                "elixir-fr-sdp-2019"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0654",
                "http://edamontology.org/topic_3168",
                "http://edamontology.org/topic_3071",
                "http://edamontology.org/topic_0091"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Leena Salmela",
                    "email": "leena.salmela@cs.Helsinki.FI",
                    "url": "https://www.cs.helsinki.fi/u/lmsalmel/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Eric Rivals",
                    "email": "rivals@lirmm.fr",
                    "url": "http://www.lirmm.fr/~rivals/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "LIRMM",
                    "email": null,
                    "url": "http://www.lirmm.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "http://www.atgc-montpellier.fr/lordec/",
            "maturity": "Mature",
            "cost": null,
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-25T14:01:03.046535Z",
            "teams": [
                "ATGC"
            ],
            "source_repository": null
        },
        {
            "id": 145,
            "name": "MacSyFinder",
            "description": "Program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems to reflect these conserved features, and to allow their efficient detection.",
            "homepage": "https://github.com/gem-pasteur/macsyfinder",
            "biotoolsID": "macsyfinder",
            "biotoolsCURIE": "biotools:macsyfinder",
            "tool_type": [
                "Web application",
                "Command-line tool"
            ],
            "collection": [
                "GEM Pasteur"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0085"
            ],
            "primary_publication": [
                "10.1371/journal.pone.0110726",
                "10.24072/pcjournal.250"
            ],
            "operating_system": [
                "Linux",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Bertrand Néron",
                    "email": "bneron@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Eduardo Rocha",
                    "email": "eduardo.rocha@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/eduardo-rocha/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Bioinformatics and Biostatistics HUB",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "Microbial Evolutionary Genomics Unit",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": "CNRS - UMR 352"
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Bertrand Néron",
                    "email": "bneron@pasteur.fr",
                    "url": "https://research.pasteur.fr/en/member/bertrand-neron/",
                    "orcidid": "https://orcid.org/0000-0002-0220-0482",
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Eduardo Rocha",
                    "email": "eduardo.rocha@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/eduardo-rocha/",
                    "orcidid": "https://orcid.org/0000-0001-7704-822X",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Bertrand Néron",
                    "email": "bneron@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Sophie Abby",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-5231-3346",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "Institut Pasteur",
                    "email": null,
                    "url": "https://research.pasteur.fr",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "C3BI",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/center/c3bi/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": null
                }
            ],
            "tool_licence": "GPL-3.0",
            "documentation": "https://macsyfinder.readthedocs.io/en/latest/",
            "maturity": "Mature",
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-24T13:49:36.708539Z",
            "teams": [
                "Pasteur HUB"
            ],
            "source_repository": "https://github.com/gem-pasteur/macsyfinder"
        },
        {
            "id": 143,
            "name": "leBIBI",
            "description": "Quick bioInformatic phylogeny of prokaryotes.",
            "homepage": "https://umr5558-bibiserv.univ-lyon1.fr/lebibi/lebibi.cgi",
            "biotoolsID": "leBIBI",
            "biotoolsCURIE": "biotools:leBIBI",
            "tool_type": [],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0084"
            ],
            "primary_publication": [],
            "operating_system": [],
            "tool_credit": [],
            "tool_licence": null,
            "documentation": null,
            "maturity": null,
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 154145,
            "last_update": "2019-11-06T11:33:13Z",
            "teams": [
                "PRABI-Lyon-Grenoble"
            ],
            "source_repository": null
        },
        {
            "id": 243,
            "name": "RAPPAS",
            "description": "RAPPAS stands for Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences. It uses an alignment-free approach for phylogenetic placement, thus removing the hurdle of query sequence alignment.",
            "homepage": "http://www.atgc-montpellier.fr/RAPPAS/",
            "biotoolsID": "RAPPAS",
            "biotoolsCURIE": "biotools:RAPPAS",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0091",
                "http://edamontology.org/topic_0637",
                "http://edamontology.org/topic_3293",
                "http://edamontology.org/topic_3174"
            ],
            "primary_publication": [
                "10.1093/bioinformatics/btz068"
            ],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Benjamin Linard",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "https://github.com/blinard-BIOINFO/RAPPAS",
            "maturity": "Emerging",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T20:59:27.880847Z",
            "teams": [],
            "source_repository": null
        },
        {
            "id": 92,
            "name": "RARe",
            "description": "RARe is a research infrastructure registered on the french national roadmap that brings together five networks of BRCs conserving genetic, genomic, and biological resources assembled and characterized by research on domestic animals, model or cultivated plants, wild species related to domestic animals, forest trees, micro-organisms of agronomic or agri-food interest, micro-organisms and environmental organisms.\nThe purpose of this web portal is to facilitate the discoverability of these data. \nRARe search is an implementation of DataDiscovery.",
            "homepage": "https://urgi.versailles.inrae.fr/rare/",
            "biotoolsID": "RARe",
            "biotoolsCURIE": "biotools:RARe",
            "tool_type": [
                "Database portal",
                "Web service",
                "Web API",
                "Web application"
            ],
            "collection": [
                "elixir-fr-sdp-2019",
                "URGI"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0780",
                "http://edamontology.org/topic_0610",
                "http://edamontology.org/topic_3071",
                "http://edamontology.org/topic_0091",
                "http://edamontology.org/topic_3810"
            ],
            "primary_publication": [],
            "operating_system": [],
            "tool_credit": [
                {
                    "type_role": [
                        "Support",
                        "Primary contact"
                    ],
                    "name": "Support service",
                    "email": "urgi-support@inrae.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                }
            ],
            "tool_licence": "BSD-3-Clause",
            "documentation": "https://urgi.versailles.inrae.fr/rare/about",
            "maturity": "Emerging",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-09-02T05:04:36.924340Z",
            "teams": [
                "PlantBioinfoPF"
            ],
            "source_repository": null
        },
        {
            "id": 119,
            "name": "RSAT suite",
            "description": "Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialised tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows.",
            "homepage": "http://rsat.eu",
            "biotoolsID": "rsat",
            "biotoolsCURIE": "biotools:rsat",
            "tool_type": [
                "Web application",
                "Suite"
            ],
            "collection": [
                "elixir-fr-sdp-2019",
                "Animal and Crop Genomics"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0621",
                "http://edamontology.org/topic_0749",
                "http://edamontology.org/topic_0203",
                "http://edamontology.org/topic_3512",
                "http://edamontology.org/topic_3125"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Jacques van Helden",
                    "email": "Jacques.van-Helden@univ-amu.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "Other",
            "documentation": "http://rsat.eu",
            "maturity": null,
            "cost": null,
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-25T14:00:33.330732Z",
            "teams": [
                "TAGC-BU"
            ],
            "source_repository": null
        },
        {
            "id": 110,
            "name": "RSAT retrieve-ensembl-seq",
            "description": "Returns upstream, downstream, intronic, exonic, UTR, transcript, mRNA, CDS or gene sequences for a list of genes from the EnsEMBL database.\nMulti-genome queries are supported: automatic retrieval of sequences for all the orthologs of the query genes, at a given taxonomical level.",
            "homepage": "http://rsat.sb-roscoff.fr/retrieve-ensembl-seq_form.cgi",
            "biotoolsID": "rsat-retrieve-ensembl-seq",
            "biotoolsCURIE": "biotools:rsat-retrieve-ensembl-seq",
            "tool_type": [
                "Web service",
                "Web application",
                "Command-line tool"
            ],
            "collection": [
                "elixir-fr-sdp-2019",
                "FR",
                "Regulatory Sequence Analysis Tools (RSAT)"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0204",
                "http://edamontology.org/topic_3511",
                "http://edamontology.org/topic_0749"
            ],
            "primary_publication": [
                "10.1093/bioinformatics/btp519"
            ],
            "operating_system": [
                "Linux",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [],
                    "name": "Université Libre de Bruxelles",
                    "email": null,
                    "url": "https://www.ulb.be/",
                    "orcidid": null,
                    "gridid": "grid.4989.c",
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Morgane Thomas-Chollier",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-2608-476X",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Documentor",
                        "Maintainer",
                        "Support",
                        "Developer",
                        "Primary contact"
                    ],
                    "name": "Olivier Sand",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-1465-1640",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "AFL-3.0",
            "documentation": "https://rsat-doc.github.io/using-RSAT/",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2020-06-16T10:55:27Z",
            "teams": [],
            "source_repository": "https://github.com/rsat-doc"
        },
        {
            "id": 138,
            "name": "SARTools",
            "description": "R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis.",
            "homepage": "https://github.com/PF2-pasteur-fr/SARTools",
            "biotoolsID": "sartools",
            "biotoolsCURIE": "biotools:sartools",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [
                "SARTools"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_2269",
                "http://edamontology.org/topic_3308"
            ],
            "primary_publication": [
                "10.1371/journal.pone.0157022"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Developer",
                        "Primary contact"
                    ],
                    "name": "Marie-Agnès Dillies",
                    "email": "marie-agnes.dillies@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/marie-agnes-dillies/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "Institut Pasteur",
                    "email": null,
                    "url": "https://research.pasteur.fr",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Support",
                        "Primary contact"
                    ],
                    "name": "Jean-Yves Coppée",
                    "email": "jean-yves.coppee@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/jean-yves-coppee/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "C3BI",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/center/c3bi/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "Bioinformatics and Biostatistics Hub",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer",
                        "Primary contact"
                    ],
                    "name": "Hugo Varet",
                    "email": "hugo.varet@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/hugo-varet/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Contributor"
                    ],
                    "name": "France Génomique",
                    "email": null,
                    "url": "https://www.france-genomique.org",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Funding agency",
                    "note": null
                }
            ],
            "tool_licence": "GPL-2.0",
            "documentation": "https://github.com/PF2-pasteur-fr/SARTools",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2021-04-17T15:12:05Z",
            "teams": [
                "Pasteur HUB"
            ],
            "source_repository": "https://github.com/PF2-pasteur-fr/SARTools"
        },
        {
            "id": 147,
            "name": "SortMeRNA",
            "description": "Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.",
            "homepage": "https://bioinfo.cristal.univ-lille.fr/RNA/sortmerna/",
            "biotoolsID": "sortmerna",
            "biotoolsCURIE": "biotools:sortmerna",
            "tool_type": [
                "Web application",
                "Command-line tool"
            ],
            "collection": [
                "ELIXIR Trainer Tools"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3308",
                "http://edamontology.org/topic_3941",
                "http://edamontology.org/topic_3174"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": null,
                    "email": null,
                    "url": "https://github.com/biocore/sortmerna/issues",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": null,
                    "email": null,
                    "url": "https://github.com/sortmerna/sortmerna/issues",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "https://github.com/sortmerna/sortmerna/wiki/User-manual-v4.3.2",
            "maturity": null,
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-24T14:49:42.747317Z",
            "teams": [
                "Bilille"
            ],
            "source_repository": null
        },
        {
            "id": 181,
            "name": "CARNAC",
            "description": "Server which predicts conserved secondary structure elements of homologous RNAs.  The input of a set of RNA sequences are not required to be previously aligned.",
            "homepage": "http://bioinfo.lifl.fr/carnac",
            "biotoolsID": "carnac",
            "biotoolsCURIE": "biotools:carnac",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0099",
                "http://edamontology.org/topic_0082",
                "http://edamontology.org/topic_0097",
                "http://edamontology.org/topic_0659",
                "http://edamontology.org/topic_0781"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Carnac team",
                    "email": "carnac@univ-lille1.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "http://bioinfo.lifl.fr/carnac/help.php",
            "maturity": null,
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-25T14:52:06.002489Z",
            "teams": [
                "Bilille"
            ],
            "source_repository": null
        },
        {
            "id": 137,
            "name": "SHAMAN",
            "description": "SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. It is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016]. It robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].",
            "homepage": "http://shaman.c3bi.pasteur.fr/",
            "biotoolsID": "shaman",
            "biotoolsCURIE": "biotools:shaman",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_3174"
            ],
            "primary_publication": [
                "10.1073/pnas.1523899113"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Pierre Lechat",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/member/pierre-lechat/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Amine Ghozlane",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/member/amine-ghozlane/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "Institut Pasteur",
                    "email": null,
                    "url": "https://research.pasteur.fr",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "C3BI",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/center/c3bi/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "Bioinformatics and Biostatistics Hub",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "SHAMAN team",
                    "email": "shaman@pasteur.fr",
                    "url": "https://research.pasteur.fr/en/software/shaman-shiny-application-for-metagenomic-analysis/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Stevenn Volant",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/member/stevenn-volant/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Hugo Varet",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/member/hugo-varet/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "GPL-3.0",
            "documentation": "http://shaman.c3bi.pasteur.fr/",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 742,
            "citations": null,
            "annual_visits": 1855,
            "last_update": "2019-01-15T02:26:44Z",
            "teams": [
                "Pasteur HUB"
            ],
            "source_repository": "https://github.com/aghozlane/shaman"
        },
        {
            "id": 132,
            "name": "Minia",
            "description": "Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.",
            "homepage": "http://minia.genouest.org/",
            "biotoolsID": "minia",
            "biotoolsCURIE": "biotools:minia",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [
                "GATB"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0196"
            ],
            "primary_publication": [
                "10.1186/1748-7188-9-2"
            ],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Guillaume Rizk",
                    "email": "guillaume.rizk@irisa.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Rayan Chikhi",
                    "email": "chikhi@psu.edu",
                    "url": "http://rayan.chikhi.name",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "GenOuest",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                }
            ],
            "tool_licence": "CECILL-2.0",
            "documentation": "http://minia.genouest.org/files/minia.pdf",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-24T14:36:01.515486Z",
            "teams": [
                "GenOuest"
            ],
            "source_repository": null
        },
        {
            "id": 140,
            "name": "NucleusJ",
            "description": "Simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D.",
            "homepage": "http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start",
            "biotoolsID": "nucleusj",
            "biotoolsCURIE": "biotools:nucleusj",
            "tool_type": [
                "Desktop application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0097",
                "http://edamontology.org/topic_2229",
                "http://edamontology.org/topic_3382"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Axel Poulet",
                    "email": "pouletaxel@gmail.com",
                    "url": "http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start#authors",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start#usage",
            "maturity": null,
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-25T15:54:14.614349Z",
            "teams": [
                "AuBi"
            ],
            "source_repository": null
        },
        {
            "id": 197,
            "name": "JASS",
            "description": "software package that handles the computation of the joint statistics over sets of selected GWAS results, and the interactive exploration of the results through a web interface.",
            "homepage": "http://statistical-genetics.pages.pasteur.fr/jass/",
            "biotoolsID": "jass",
            "biotoolsCURIE": "biotools:jass",
            "tool_type": [
                "Command-line tool",
                "Web application",
                "Web service"
            ],
            "collection": [
                "Institut Pasteur"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3517",
                "http://edamontology.org/topic_2269",
                "http://edamontology.org/topic_3053"
            ],
            "primary_publication": [
                "10.1093/nargab/lqaa003",
                "10.1101/714832v1"
            ],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Pierre Lechat",
                    "email": "pierre.lechat@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/pierre-lechat/",
                    "orcidid": "https://orcid.org/0000-0003-1050-5582",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Carla Lasry",
                    "email": null,
                    "url": "https://research.pasteur.fr/fr/member/carla-lasry/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Contributor"
                    ],
                    "name": "Chunzi Yao",
                    "email": "chunzi.yao@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/chunzi-yao/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Contributor"
                    ],
                    "name": "Vincent Laville",
                    "email": "vincent.laville@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Contributor"
                    ],
                    "name": "Bjarni Vilhjalmsson",
                    "email": null,
                    "url": "https://pure.au.dk/portal/en/persons/bjarni-johann-vilhjlmsson(35c047ab-0899-4434-91bb-121e4878ec76).html",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Hervé Ménager",
                    "email": "herve.menager@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/search/herve%20menager",
                    "orcidid": "https://orcid.org/0000-0002-7552-1009",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Hugues Aschard",
                    "email": "hugues.aschard@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/hugues-aschard/",
                    "orcidid": "http://orcid.org/0000-0002-7554-6783",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Hanna Julienne",
                    "email": "hanna.julienne@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/hanna-julienne/",
                    "orcidid": "https://orcid.org/0000-0001-8214-9412",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Vincent Guillemot",
                    "email": "vincent.guillemot@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/vincent-guillemot/",
                    "orcidid": "https://orcid.org/0000-0002-7421-0655",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "http://statistical-genetics.pages.pasteur.fr/jass/",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T14:46:08.475046Z",
            "teams": [],
            "source_repository": "https://gitlab.pasteur.fr/statistical-genetics/jass"
        }
    ]
}