HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 233,
"next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=120&ordering=primary_publication",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=80&ordering=primary_publication",
"results": [
{
"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": 242,
"name": "WAVES",
"description": "WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications. In order to fulfill the service’s computational needs, WAVES can perform computation on various resources and environments, such as Galaxy instances.",
"homepage": "http://www.atgc-montpellier.fr/waves/",
"biotoolsID": "WAVES",
"biotoolsCURIE": "biotools:WAVES",
"tool_type": [
"Web API",
"Web application",
"Web service",
"Bioinformatics portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_3372"
],
"primary_publication": [
"10.1093/bioinformatics/bty639"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "LIRMM",
"email": null,
"url": "http://www.lirmm.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer",
"Maintainer"
],
"name": "Marc Chakiachvili",
"email": "mchakiachvili@ebi.ac.uk",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact",
"Contributor"
],
"name": "Vincent Lefort",
"email": "vincent.lefort@lirmm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://waves-core.readthedocs.io/",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [],
"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": 244,
"name": "NGphylogeny.fr",
"description": "Free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.",
"homepage": "https://ngphylogeny.fr/",
"biotoolsID": "NGphylogeny.fr",
"biotoolsCURIE": "biotools:NGphylogeny.fr",
"tool_type": [
"Web application",
"Workflow",
"Bioinformatics portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0091"
],
"primary_publication": [
"10.1093/nar/gkz303"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer",
"Maintainer",
"Primary contact"
],
"name": "Frédéric Lemoine",
"email": "frederic.lemoine@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Damien Correia",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Fabien Mareuil",
"email": "fmareuil@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact",
"Contributor"
],
"name": "Vincent Lefort",
"email": "vincent.lefort@lirmm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://ngphylogeny.fr/documentation",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:31.390401Z",
"teams": [],
"source_repository": null
},
{
"id": 255,
"name": "Kmerator",
"description": "Kmerator is a prototype tool designed for the prediction of specific k-mers (also called tags) from input sequences, considering a reference genome and an ENSEMBL-like transcriptome. From these specific k-mers, it also outputs their corresponding specific contigs which are sequences of consecutive k-mers (overlapping length between k-mers must be k-1, otherwise, it's a new contig). Kmerator first uses Jellyfish to create 2 requestable indexes from the reference genome and transcriptome, and second, decomposes your input transcript or gene sequences to count the occurences of each k-mer in the genome and transcriptome.",
"homepage": "https://github.com/Transipedia/kmerator",
"biotoolsID": "kmerator",
"biotoolsCURIE": "biotools:kmerator",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3360",
"http://edamontology.org/topic_0659",
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_3170",
"http://edamontology.org/topic_3512"
],
"primary_publication": [
"10.1093/nargab/lqab058"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Thérèse Commes",
"email": "therese.commes@inserm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T16:01:46.602609Z",
"teams": [
"Bio2M"
],
"source_repository": null
},
{
"id": 249,
"name": "FROGS",
"description": "The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.",
"homepage": "http://frogs.toulouse.inra.fr/",
"biotoolsID": "frogs",
"biotoolsCURIE": "biotools:frogs",
"tool_type": [
"Command-line tool"
],
"collection": [
"FROGS"
],
"scientific_topics": [
"http://edamontology.org/topic_3697",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_3174",
"http://edamontology.org/topic_0637",
"http://edamontology.org/topic_3168"
],
"primary_publication": [
"10.1093/bioinformatics/btx791",
"10.1093/bib/bbab318"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Géraldine Pascal",
"email": "geraldine.pascal@inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Géraldine Pascal",
"email": "geraldine.pascal@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://github.com/geraldinepascal/FROGS",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:07:18.846597Z",
"teams": [
"MIGALE"
],
"source_repository": "https://github.com/geraldinepascal/FROGS"
},
{
"id": 107,
"name": "GENOMICUS",
"description": "Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "http://www.genomicus.biologie.ens.fr/genomicus/",
"biotoolsID": "GENOMICUS",
"biotoolsCURIE": "biotools:GENOMICUS",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0623"
],
"primary_publication": [
"10.1093/bioinformatics/btq079",
"10.1093/nar/gkab1091"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "IBENS - DYOGEN Team",
"email": null,
"url": "http://www.ibens.ens.fr/?rubrique43&lang=en",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "PB-IBENS",
"email": null,
"url": "https://www.ibens.ens.fr/?rubrique55",
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://www.youtube.com/watch?v=CokUh3fUbGQ",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2023-03-06T14:10:23.175189Z",
"teams": [
"PB-IBENS"
],
"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": 176,
"name": "Galaxy",
"description": "Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.",
"homepage": "https://galaxyproject.org/",
"biotoolsID": "galaxy",
"biotoolsCURIE": "biotools:galaxy",
"tool_type": [
"Workflow",
"Bioinformatics portal",
"Web application",
"Web API"
],
"collection": [
"Galaxy",
"Animal and Crop Genomics"
],
"scientific_topics": [
"http://edamontology.org/topic_3673",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_0196",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622"
],
"primary_publication": [
"10.1093/nar/gkw343",
"10.1093/nar/gkac247"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Galaxy support",
"email": null,
"url": "https://biostar.usegalaxy.org/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Galaxy Community",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": null
}
],
"tool_licence": "AFL-3.0",
"documentation": "https://usegalaxy.org/api/docs",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 400,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T14:46:57.861339Z",
"teams": [
"South Green"
],
"source_repository": "https://github.com/galaxyproject/galaxy"
},
{
"id": 258,
"name": "FAIR-Checker",
"description": "FAIR-Checker is a tool aimed at assessing FAIR principles and empowering data provider to enhance the quality of their digital resources. Data providers and consumers can check how FAIR are web resources. Developers can explore and inspect metadata exposed in web resources.",
"homepage": "https://fair-checker.france-bioinformatique.fr",
"biotoolsID": "fair-checker",
"biotoolsCURIE": "biotools:fair-checker",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3316",
"http://edamontology.org/topic_0089"
],
"primary_publication": [
"10.1186/s13326-023-00289-5"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:45:19.260708Z",
"teams": [
"IFB Core",
"BiRD"
],
"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": "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
},
{
"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
}
],
"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"
},
{
"id": 261,
"name": "Panache",
"description": "Panache (Pangenome analyzer with chromosomal exploration) is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show aresence/absence information of pangenomic blocks of sequence or genes in a browser-like display.",
"homepage": "http://github.com/SouthGreenPlatform/panache",
"biotoolsID": "panache",
"biotoolsCURIE": "biotools:panache",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0654",
"http://edamontology.org/topic_0621"
],
"primary_publication": [
"10.1093/bioinformatics/btab688"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Mathieu Rouard",
"email": "m.rouard@cgiar.org",
"url": null,
"orcidid": "https://orcid.org/0000-0003-0284-1885",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Éloi Durant",
"email": "eloi.durant@ird.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-2734-4327",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-11-01T10:14:54.337479Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 263,
"name": "TrEMOLO",
"description": "Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.",
"homepage": "https://github.com/DrosophilaGenomeEvolution/TrEMOLO",
"biotoolsID": "tremolo",
"biotoolsCURIE": "biotools:tremolo",
"tool_type": [
"Workflow",
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0798",
"http://edamontology.org/topic_0196",
"http://edamontology.org/topic_3168",
"http://edamontology.org/topic_3175"
],
"primary_publication": [
"10.1186/s13059-023-02911-2"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [],
"name": "Anna-Sophie Fiston-Lavier",
"email": "anna-sophie.fiston-lavier@umontpellier.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-7306-6532",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Séverine Chambeyron",
"email": "severine.chambeyron@igh.cnrs.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-2775-6556",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:41:13.039486Z",
"teams": [
"South Green"
],
"source_repository": "https://dataverse.ird.fr/dataverse/tremolo_data"
},
{
"id": 266,
"name": "LedPred",
"description": "This package creates a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, NGS peaks and signals and other numerical scores of the sequences using supervised classification. It contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences.",
"homepage": "http://bioconductor.org/packages/release/bioc/html/LedPred.html",
"biotoolsID": "ledpred",
"biotoolsCURIE": "biotools:ledpred",
"tool_type": [
"Command-line tool",
"Library"
],
"collection": [
"BioConductor"
],
"scientific_topics": [
"http://edamontology.org/topic_3168",
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_3474"
],
"primary_publication": [
"10.1093/bioinformatics/btv705"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Aitor Gonzalez",
"email": "aitor.gonzalez@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://bioconductor.org/packages/release/bioc/html/LedPred.html",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T15:20:13.683529Z",
"teams": [
"TAGC-BU"
],
"source_repository": null
},
{
"id": 267,
"name": "ReMap",
"description": "ReMap is a large scale integrative analysis of DNA-binding experiments for Homo sapiens, Mus musculus, Drosophila melanogaster and Arabidopsis thaliana transcriptional regulators. The catalogues are the results of the manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources (GEO, ENCODE, ENA). ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers.",
"homepage": "https://remap.univ-amu.fr/",
"biotoolsID": "inserm-remap",
"biotoolsCURIE": "biotools:inserm-remap",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0102",
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_3173"
],
"primary_publication": [
"10.1093/nar/gku1280",
"10.1093/nar/gkab996",
"10.1093/nar/gkz945",
"10.1093/nar/gkx1092"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": "Inserm U1090 - TAGC",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "Aix-Marseille University",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "French Institute of Health and Medical Research",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer",
"Primary contact"
],
"name": "Benoit Ballester",
"email": "benoit.ballester@inserm.fr",
"url": null,
"orcidid": "http://orcid.org/0000-0002-0834-7135",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://remap.univ-amu.fr/about_hsap_page",
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:21:26.315951Z",
"teams": [
"TAGC-BU"
],
"source_repository": "https://remap.univ-amu.fr/"
},
{
"id": 267,
"name": "ReMap",
"description": "ReMap is a large scale integrative analysis of DNA-binding experiments for Homo sapiens, Mus musculus, Drosophila melanogaster and Arabidopsis thaliana transcriptional regulators. The catalogues are the results of the manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources (GEO, ENCODE, ENA). ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers.",
"homepage": "https://remap.univ-amu.fr/",
"biotoolsID": "inserm-remap",
"biotoolsCURIE": "biotools:inserm-remap",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0102",
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_3173"
],
"primary_publication": [
"10.1093/nar/gku1280",
"10.1093/nar/gkab996",
"10.1093/nar/gkz945",
"10.1093/nar/gkx1092"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": "Inserm U1090 - TAGC",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "Aix-Marseille University",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "French Institute of Health and Medical Research",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer",
"Primary contact"
],
"name": "Benoit Ballester",
"email": "benoit.ballester@inserm.fr",
"url": null,
"orcidid": "http://orcid.org/0000-0002-0834-7135",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://remap.univ-amu.fr/about_hsap_page",
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:21:26.315951Z",
"teams": [
"TAGC-BU"
],
"source_repository": "https://remap.univ-amu.fr/"
},
{
"id": 267,
"name": "ReMap",
"description": "ReMap is a large scale integrative analysis of DNA-binding experiments for Homo sapiens, Mus musculus, Drosophila melanogaster and Arabidopsis thaliana transcriptional regulators. The catalogues are the results of the manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources (GEO, ENCODE, ENA). ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers.",
"homepage": "https://remap.univ-amu.fr/",
"biotoolsID": "inserm-remap",
"biotoolsCURIE": "biotools:inserm-remap",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0102",
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_3173"
],
"primary_publication": [
"10.1093/nar/gku1280",
"10.1093/nar/gkab996",
"10.1093/nar/gkz945",
"10.1093/nar/gkx1092"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": "Inserm U1090 - TAGC",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "Aix-Marseille University",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "French Institute of Health and Medical Research",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer",
"Primary contact"
],
"name": "Benoit Ballester",
"email": "benoit.ballester@inserm.fr",
"url": null,
"orcidid": "http://orcid.org/0000-0002-0834-7135",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://remap.univ-amu.fr/about_hsap_page",
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:21:26.315951Z",
"teams": [
"TAGC-BU"
],
"source_repository": "https://remap.univ-amu.fr/"
},
{
"id": 267,
"name": "ReMap",
"description": "ReMap is a large scale integrative analysis of DNA-binding experiments for Homo sapiens, Mus musculus, Drosophila melanogaster and Arabidopsis thaliana transcriptional regulators. The catalogues are the results of the manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources (GEO, ENCODE, ENA). ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers.",
"homepage": "https://remap.univ-amu.fr/",
"biotoolsID": "inserm-remap",
"biotoolsCURIE": "biotools:inserm-remap",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0102",
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_3173"
],
"primary_publication": [
"10.1093/nar/gku1280",
"10.1093/nar/gkab996",
"10.1093/nar/gkz945",
"10.1093/nar/gkx1092"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": "Inserm U1090 - TAGC",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "Aix-Marseille University",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "French Institute of Health and Medical Research",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer",
"Primary contact"
],
"name": "Benoit Ballester",
"email": "benoit.ballester@inserm.fr",
"url": null,
"orcidid": "http://orcid.org/0000-0002-0834-7135",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://remap.univ-amu.fr/about_hsap_page",
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:21:26.315951Z",
"teams": [
"TAGC-BU"
],
"source_repository": "https://remap.univ-amu.fr/"
},
{
"id": 279,
"name": "FINSURF",
"description": "FINSURF (Functional Identification of Non-coding Sequences Using Random Forests) is a tool designed to analyse lists of sequences variants in the human genome.\nIt assigns a score to each variant, reflecting its functional importance and therefore its likelihood to disrupt the physiology of its carrier. FINSURF scores Single Nucleotide Variants (SNV), insertions and deletions. Among SNVs, transitions and transversions are treated separately. Insertions are characterised by a score given to each base flanking the insertion point. Deletions are characterised by a score at every deleted base. FINSURF can (optionally) use a list of known or suspected disease genes, in order to restrict results to variants overlapping cis-regulatory elements linked to these genes.\n\nFor a variant of interest, users can generate a graphical representation of \"feature contributions », showing the relative contributions of genomic, functional or evolutionary information to its score.",
"homepage": "https://www.finsurf.bio.ens.psl.eu/",
"biotoolsID": "finsurf",
"biotoolsCURIE": "biotools:finsurf",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3673",
"http://edamontology.org/topic_3577",
"http://edamontology.org/topic_3300"
],
"primary_publication": [
"10.1371/journal.pgen.1010191"
],
"operating_system": [
"Mac",
"Linux"
],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "finsurf@bio.ens.psl.eu",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "IBENS - DYOGEN Team",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@bio.ens.psl.eu",
"url": null,
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Lambert Moyon",
"email": "moyon@bio.ens.psl.eu",
"url": null,
"orcidid": "https://orcid.org/0000-0003-2390-3942",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Alexandra Louis",
"email": "alexandra.louis@bio.ens.psl.eu",
"url": null,
"orcidid": "https://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Camille Berthelot",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-5054-2690",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:55:59.341655Z",
"teams": [
"PB-IBENS"
],
"source_repository": "https://github.com/DyogenIBENS/FINSURF/"
},
{
"id": 282,
"name": "easy16S",
"description": "Easy16S is designed to facilitate the exploration, visualization, and analysis of microbiome data.",
"homepage": "https://easy16s.migale.inrae.fr/",
"biotoolsID": "easy16s",
"biotoolsCURIE": "biotools:easy16s",
"tool_type": [],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3174"
],
"primary_publication": [
"10.21105/joss.06704"
],
"operating_system": [
"Mac",
"Windows",
"Linux"
],
"tool_credit": [
{
"type_role": [],
"name": "Cédric Midoux",
"email": "cedric.midoux@inrae.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-7964-0929",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://easy16s.migale.inrae.fr/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-12-11T14:36:21.065324Z",
"teams": [
"MIGALE"
],
"source_repository": "https://doi.org/10.57745/ZN1HXQ"
}
]
}