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=180&ordering=description",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=140&ordering=description",
"results": [
{
"id": 280,
"name": "Paraload",
"description": "Paraload is an original utility which ensures job distribution between thousands of processors, according to the type of the data to be analysed.",
"homepage": "ftp://doua.prabi.fr/pub/logiciel/paraload",
"biotoolsID": "Paraload",
"biotoolsCURIE": "biotools:Paraload",
"tool_type": [],
"collection": [],
"scientific_topics": [],
"primary_publication": [],
"operating_system": [],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2019-11-06T12:00:30Z",
"teams": [
"PRABI-AMSB"
],
"source_repository": null
},
{
"id": 175,
"name": "Logol",
"description": "Pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic).",
"homepage": "http://logol.genouest.org",
"biotoolsID": "logol",
"biotoolsCURIE": "biotools:logol",
"tool_type": [
"Command-line tool",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0160"
],
"primary_publication": [
"10.1007/978-3-319-09192-1_4"
],
"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": "GenOuest",
"email": "support@genouest.org",
"url": "http://www.genouest.org",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "CECILL-2.0",
"documentation": "http://training.genouest.org/claroline/claroline/learnPath/learningPathList.php?cidReset=true&cidReq=LOGOL",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2018-12-10T12:58:34Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 163,
"name": "PEP-FOLD",
"description": "PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution. Updates to PEP-FOLD allow for modeling of linear and disulphide bonded cyclic peptides with 9-36 amino acids using benchmarked peptides.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD3",
"biotoolsID": "pep-fold",
"biotoolsCURIE": "biotools:pep-fold",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2275"
],
"primary_publication": [
"10.1093/nar/gkp323",
"10.1093/nar/gks419",
"10.1093/nar/gkw329"
],
"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-FOLD3",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 3900,
"citations": null,
"annual_visits": 30000,
"last_update": "2024-11-24T20:59:57.942237Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"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": [
"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
},
{
"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": "http://stephaneguindon.github.io/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"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": "Eric Rivals",
"email": "rivals@lirmm.fr",
"url": "http://www.lirmm.fr/~rivals/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"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": [
"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_0091",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_3810"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Support"
],
"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": "2025-07-29T13:42:40.608985Z",
"teams": [
"URGI"
],
"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_3125",
"http://edamontology.org/topic_3512"
],
"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": 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": 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": [
"Primary contact",
"Developer",
"Documentor",
"Maintainer",
"Support"
],
"name": "Olivier Sand",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0003-1465-1640",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"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
}
],
"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": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "https://research.pasteur.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"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
},
{
"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": [
"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": [
"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": [],
"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
}
],
"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_0097",
"http://edamontology.org/topic_0659",
"http://edamontology.org/topic_0099",
"http://edamontology.org/topic_0082",
"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
}
]
}