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            "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",
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                "Windows",
                "Mac"
            ],
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                        "Provider"
                    ],
                    "name": "Institut Pasteur",
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                    "url": "https://research.pasteur.fr",
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                        "Primary contact"
                    ],
                    "name": "Marie-Agnès Dillies",
                    "email": "marie-agnes.dillies@pasteur.fr",
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                },
                {
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                        "Support",
                        "Primary contact"
                    ],
                    "name": "Jean-Yves Coppée",
                    "email": "jean-yves.coppee@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/jean-yves-coppee/",
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                        "Primary contact"
                    ],
                    "name": "Hugo Varet",
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                    "name": "C3BI",
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                    "url": "https://research.pasteur.fr/en/center/c3bi/",
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                        "Provider"
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            "annual_visits": 0,
            "last_update": "2021-04-17T15:12:05Z",
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            "id": 90,
            "name": "FAIDARE",
            "description": "FAIDARE: FAIR Data-finder for Agronomic Research. \nThe purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories.\n\nIt is based on the Breeding API (BrAPI) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface. It also provides a standard interface that can be accessed programatically through web services.\n\nIt is an extension of the generic DataDiscovery portal, a web portal that allows finding any type of data across several databases through a lightweight keyword based search. FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.",
            "homepage": "https://urgi.versailles.inrae.fr/faidare/",
            "biotoolsID": "faidare",
            "biotoolsCURIE": "biotools:faidare",
            "tool_type": [
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                "Web service",
                "Web API",
                "Web application"
            ],
            "collection": [
                "elixir-fr-sdp-2019",
                "URGI"
            ],
            "scientific_topics": [
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                "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"
            ],
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            ],
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                        "Primary contact",
                        "Support"
                    ],
                    "name": "URGI support",
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                    "url": null,
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                    "gridid": null,
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                    "note": null
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            ],
            "tool_licence": "BSD-3-Clause",
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            "citations": null,
            "annual_visits": null,
            "last_update": "2024-09-02T05:04:34.812991Z",
            "teams": [
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            "source_repository": "https://forgemia.inra.fr/urgi-is/faidare"
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            "id": 288,
            "name": "MAGNETO",
            "description": "An automated workflow for genome-resolved metagenomics",
            "homepage": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto",
            "biotoolsID": "magneto",
            "biotoolsCURIE": "biotools:magneto",
            "tool_type": [
                "Command-line tool"
            ],
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            "scientific_topics": [
                "http://edamontology.org/topic_3697",
                "http://edamontology.org/topic_0196",
                "http://edamontology.org/topic_3174",
                "http://edamontology.org/topic_0769",
                "http://edamontology.org/topic_3050"
            ],
            "primary_publication": [],
            "operating_system": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "tool_credit": [
                {
                    "type_role": [],
                    "name": "Samuel Chaffron",
                    "email": "samuel.chaffron@ls2n.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
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                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Benjamin Churcheward",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Audrey Bihouée",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
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                },
                {
                    "type_role": [],
                    "name": "Guillaume Fertin",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Hugo Lefeuvre",
                    "email": "hugo.lefeuvre@univ-nantes.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
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                }
            ],
            "tool_licence": null,
            "documentation": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto/-/wikis/home",
            "maturity": null,
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2025-02-24T16:29:20.503951Z",
            "teams": [
                "BiRD"
            ],
            "source_repository": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto"
        },
        {
            "id": 262,
            "name": "GeMo",
            "description": "A web-based platform for the visualization and curation of genome ancestry mosaics.",
            "homepage": "https://gemo.southgreen.fr/",
            "biotoolsID": "gemo",
            "biotoolsCURIE": "biotools:gemo",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
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                "http://edamontology.org/topic_0625",
                "http://edamontology.org/topic_3810",
                "http://edamontology.org/topic_0780",
                "http://edamontology.org/topic_3500"
            ],
            "primary_publication": [],
            "operating_system": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "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",
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                },
                {
                    "type_role": [],
                    "name": "Marilyne Summo",
                    "email": "marilyne.summo@cirad.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-9308-974X",
                    "gridid": null,
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                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Gaëtan Droc",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-1849-1269",
                    "gridid": null,
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                    "type_role": [],
                    "name": "Guillaume Martin",
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                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-1801-7500",
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            "documentation": "https://gemo.readthedocs.io",
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            "cost": "Free of charge",
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            "citations": null,
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            "last_update": "2024-11-24T15:31:16.942311Z",
            "teams": [
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            ],
            "source_repository": "https://github.com/SouthGreenPlatform/GeMo"
        },
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            "id": 144,
            "name": "SynTView",
            "description": "Comparative and interactive viewer for microbial genomes, designed to run as either a web-based tool (Flash technology) or a desktop application (AIR environment). The basis of the program is a generic genome browser with sub-maps holding information about genomic objects. The software is characterized by the presentation of syntenic organisations of microbial genomes and the visualization of polymorphism data along these genomes; these features are accessible to the user in an integrated way.",
            "homepage": "http://genopole.pasteur.fr/SynTView/",
            "biotoolsID": "syntview",
            "biotoolsCURIE": "biotools:syntview",
            "tool_type": [
                "Web application",
                "Desktop application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_3168",
                "http://edamontology.org/topic_0797"
            ],
            "primary_publication": [
                "10.1186/1471-2105-14-277"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
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                        "Primary contact"
                    ],
                    "name": null,
                    "email": "plechat@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "LGPL-3.0",
            "documentation": "http://hub18.hosting.pasteur.fr/SynTView/documentation/",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2021-05-19T14:52:04Z",
            "teams": [
                "Pasteur HUB"
            ],
            "source_repository": null
        },
        {
            "id": 238,
            "name": "TOXsIgN",
            "description": "The TOXicogenomic sIgNature (TOXsIgN) is a cross-species resource that supports online submission, storage, and retrieval of TOXicogenomic sIgNatures. TOXsIgN aims at complementing existing resources by acting as a distribution hub for the community. One of its unique features is its ability to archive heterogeneous data. TOXsIgN thus allows users to upload lists of genes positively (overexpressed for transcriptomic assays) affected and negatively (underexpressed) affected from distinct –omics experiments (e.g., transcriptomics, proteomics, or epigenomics). It also provides users with a working environment containing a powerful search engine as well as bioinformatics/biostatistics modules that enable cross-species and cross-technology signature comparisons or enrichment analyses. TOXsIgN is thus intended to serve as a warehouse for toxicogenomics and predictive toxicology tools simultaneously based on and able to analyze the overall set of signatures deposited by the community.",
            "homepage": "http://toxsign.genouest.org",
            "biotoolsID": "toxsign",
            "biotoolsCURIE": "biotools:toxsign",
            "tool_type": [
                "Web application",
                "Database portal"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_2840"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Chalmel Frédéric",
                    "email": "frederic.chalmel@univ-rennes1.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": null,
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2020-09-28T08:55:30Z",
            "teams": [],
            "source_repository": null
        },
        {
            "id": 125,
            "name": "Gigwa",
            "description": "The Gigwa application, which stands for “Genotype Investigator for Genome-Wide Analyses”, provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype patterns. It is a fairly lightweight, web-based, platform-independent solution that may be deployed on a workstation or as a data portal. It allows to feed a MongoDB database with VCF, PLINK or HapMap files containing up to tens of billions of genotypes, and provides a user-friendly interface to filter data in real time. Gigwa provides the means to export filtered data into several popular formats and features connectivity not only with online genomic tools, but also with standalone software such as FlapJack or IGV. Additionnally, Gigwa-hosted datasets are interoperable via two standard REST APIs: GA4GH and BrAPI.",
            "homepage": "http://www.southgreen.fr/content/gigwa",
            "biotoolsID": "Gigwa",
            "biotoolsCURIE": "biotools:Gigwa",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0625",
                "http://edamontology.org/topic_2885",
                "http://edamontology.org/topic_3071"
            ],
            "primary_publication": [
                "10.1093/GIGASCIENCE/GIZ051",
                "10.1186/s13742-016-0131-8"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Guilhem Sempéré",
                    "email": "guilhem.sempere@cirad.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-7429-2091",
                    "gridid": null,
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                },
                {
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                    ],
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            ],
            "tool_licence": "AGPL-3.0",
            "documentation": "http://gigwa.southgreen.fr/gigwa/docs/gigwa_docs.html",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2020-09-14T08:25:17Z",
            "teams": [
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            "source_repository": "https://github.com/SouthGreenPlatform/Gigwa2"
        },
        {
            "id": 283,
            "name": "3SRP",
            "description": "A Snakemake-based pipeline for 3' sequencing RNA profiling data analysis.  This 3’ Digital gene expression sequencing technique allows a precise and low-cost transcriptome profiling.\n\nThe main steps of the pipeline are:\n- Samples demultiplexing transform the raw paired-end fastq files into a single-end fastq file for each sample.\n- Alignment on refseq reference transcriptome is performed using bwa.\n- Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix.\nIf secondary analysis has been asked (providing a comparisons file), the expression matrix is normalized and differentially expressed genes (DEG) are searched using deseq2.\n- If DEG are found, annotation is performed using the database GO and KEGG.\n- A report is provided listing the main quality controls performed and the results found.\n\nCite : https://dx.doi.org/10.21203/rs.3.pex-1336/v1",
            "homepage": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline",
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            "biotoolsCURIE": "biotools:3SRP",
            "tool_type": [
                "Workflow"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_3308"
            ],
            "primary_publication": [
                "10.1038/s41598-017-14892-x"
            ],
            "operating_system": [
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            ],
            "tool_credit": [
                {
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                        "Provider",
                        "Support"
                    ],
                    "name": "BiRD bioinformatics facility",
                    "email": "pf-bird@univ-nantes.fr",
                    "url": "https://pf-bird.univ-nantes.fr",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact",
                        "Developer",
                        "Support"
                    ],
                    "name": "Eric Charpentier",
                    "email": "eric.charpentier@univ-nantes.fr",
                    "url": "https://pf-bird.univ-nantes.fr/about-us/members/",
                    "orcidid": "https://orcid.org/0000-0002-8571-7603",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
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                    ],
                    "name": "Dimitri MEISTERMANN",
                    "email": "dimitri.meistermann@univ-nantes.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
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                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Broad Institute",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": "Some scripts of the pipeline regarding sample demultiplexing and UMI counting have been adapated and modified from this paper:\nXiong, Y., Soumillon, M., Wu, J. et al. A Comparison of mRNA Sequencing with Random Primed and 3′-Directed Libraries. Sci Rep 7, 14626 (2017)."
                },
                {
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                        "Developer"
                    ],
                    "name": "Philippe Bordron",
                    "email": "philippe.bordron@univ-nantes.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
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                    ],
                    "name": "Solenne Dumont",
                    "email": "solenne.dumont@univ-nantes.fr",
                    "url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/",
                    "orcidid": "https://orcid.org/0000-0003-3237-7382",
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                },
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                        "Contributor"
                    ],
                    "name": "Audrey Bihouée",
                    "email": "audrey.bihouee@univ-nantes.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-8689-2083",
                    "gridid": null,
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            ],
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            "documentation": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/wikis/home",
            "maturity": "Emerging",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T14:40:06.421826Z",
            "teams": [
                "BiRD"
            ],
            "source_repository": null
        },
        {
            "id": 190,
            "name": "CRISPRFinder",
            "description": "Detects this family of direct repeats found in the DNA of many bacteria and archaea.",
            "homepage": "https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index",
            "biotoolsID": "crisprfinder",
            "biotoolsCURIE": "biotools:crisprfinder",
            "tool_type": [
                "Web application",
                "Database portal"
            ],
            "collection": [
                "CRISPR"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_2885",
                "http://edamontology.org/topic_0157",
                "http://edamontology.org/topic_0621",
                "http://edamontology.org/topic_0749",
                "http://edamontology.org/topic_0203"
            ],
            "primary_publication": [],
            "operating_system": [
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                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Marie Touchon",
                    "email": "mtouchon@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "Unlicense",
            "documentation": null,
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 480,
            "citations": null,
            "annual_visits": 2273,
            "last_update": "2024-11-24T21:05:00.924973Z",
            "teams": [
                "EBIO"
            ],
            "source_repository": null
        },
        {
            "id": 264,
            "name": "PanExplorer",
            "description": "A web-based tool for exploratory analysis and visualization of bacterial pan-genomes.",
            "homepage": "http://panexplorer.southgreen.fr",
            "biotoolsID": "panexplorer",
            "biotoolsCURIE": "biotools:panexplorer",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
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