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            "description": "The Human Splicing Finder (HSF) system combines 12 different algorithms to identify and predict mutations’ effect on splicing motifs including the acceptor and donor splice sites, the branch point and auxiliary sequences known to either enhance or repress splicing: Exonic Splicing Enhancers (ESE) and Exonic Splicing Silencers (ESS).",
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            "name": "ParameciumDB",
            "description": "Online community database for Paramecium species. Contains annotation of genome sequences and features, genome-wide data sets, advanced capabilities to query, retrieve, visualize and compare data.",
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            "biotoolsID": "parameciumdb",
            "biotoolsCURIE": "biotools:parameciumdb",
            "tool_type": [
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            "collection": [
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                "http://edamontology.org/topic_0621",
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                "Windows",
                "Mac"
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                    "name": "Terms of Use",
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            "last_update": "2024-11-25T14:00:30.463079Z",
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        },
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            "id": 8,
            "name": "Plant DataDiscovery",
            "description": "The purpose of this web portal is to facilitate the discoverability of public data on plant biology managed by different laboratories across the world.\n\nThe web portal indexes and makes findable any kind of plant data. Plant DataDiscovery is an implementation of DataDiscovery.",
            "homepage": "https://urgi.versailles.inrae.fr/data-discovery/",
            "biotoolsID": "Plant_DataDiscovery",
            "biotoolsCURIE": "biotools:Plant_DataDiscovery",
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                "Web service",
                "Web API",
                "Web application"
            ],
            "collection": [
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                "URGI"
            ],
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                "http://edamontology.org/topic_0780",
                "http://edamontology.org/topic_0091",
                "http://edamontology.org/topic_0610",
                "http://edamontology.org/topic_3810"
            ],
            "primary_publication": [
                "10.1186/s13059-018-1491-4"
            ],
            "operating_system": [],
            "tool_credit": [
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                        "Support"
                    ],
                    "name": "Support service",
                    "email": "urgi-support@inrae.fr",
                    "url": null,
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            "tool_licence": "BSD-3-Clause",
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            "maturity": "Mature",
            "cost": "Free of charge",
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            "citations": null,
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            "last_update": "2022-12-12T16:19:23.574076Z",
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        },
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            "name": "FAIDARE",
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            "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": 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",
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            "biotoolsCURIE": "biotools:kmerator",
            "tool_type": [
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                "http://edamontology.org/topic_0659",
                "http://edamontology.org/topic_0203",
                "http://edamontology.org/topic_3170",
                "http://edamontology.org/topic_3512"
            ],
            "primary_publication": [
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            ],
            "operating_system": [],
            "tool_credit": [
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                        "Primary contact"
                    ],
                    "name": "Thérèse Commes",
                    "email": "therese.commes@inserm.fr",
                    "url": null,
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            "last_update": "2024-11-24T16:01:46.602609Z",
            "teams": [
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            ],
            "source_repository": null
        },
        {
            "id": 292,
            "name": "Pan1c",
            "description": "Pan1c is a Snakemake workflow that simplifies the creation of pangenomes by focusing on the comparison of similar chromosomes, using either PGGB or Minigraph-Cactus.\nA pangenome graph is first generated individually for each chromosome, and then these chromosome-scale pangenomes are concatenated into a final graph. This approach reduces construction time through parallelization and facilitates interpretation as well as downstream analyses. Throughout the process, various graphs and statistics are produced to help users assess the quality of the pangenome graph and interpret the results.\nAll these visualizations and statistics are accessible via a web page generated by Pan1c-view.",
            "homepage": "https://forge.inrae.fr/genotoul-bioinfo/Pan1c/pan1c",
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            "biotoolsCURIE": "biotools:pan1c",
            "tool_type": [
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            "scientific_topics": [
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                "http://edamontology.org/topic_3796"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [
                {
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                        "Developer"
                    ],
                    "name": "Alexis Mergez",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
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                    "name": "Martin Racoupeau",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
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                    "note": null
                },
                {
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                        "Developer"
                    ],
                    "name": "Philippe Bardou",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-0004-0251",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
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                    ],
                    "name": "Christophe Klopp",
                    "email": "christophe.klopp@inrae.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-7126-5477",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
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                        "Provider"
                    ],
                    "name": "GenoToul bioinformatics facility",
                    "email": null,
                    "url": "https://bioinfo.genotoul.fr/",
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                    "note": null
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            ],
            "tool_licence": null,
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            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
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            "last_update": "2026-08-25T11:40:00.095755Z",
            "teams": [],
            "source_repository": "https://forge.inrae.fr/genotoul-bioinfo/Pan1c/pan1c"
        },
        {
            "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",
            "biotoolsID": "3SRP",
            "biotoolsCURIE": "biotools:3SRP",
            "tool_type": [
                "Workflow"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_3308"
            ],
            "primary_publication": [
                "10.1038/s41598-017-14892-x"
            ],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [
                {
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                        "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": [
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                    ],
                    "name": "Dimitri MEISTERMANN",
                    "email": "dimitri.meistermann@univ-nantes.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
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                    ],
                    "name": "Philippe Bordron",
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                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
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                {
                    "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)."
                },
                {
                    "type_role": [
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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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                    "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",
                    "gridid": null,
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                    "note": null
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                {
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                        "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",
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            ],
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            "documentation": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/wikis/home",
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            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T14:40:06.421826Z",
            "teams": [
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            ],
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        },
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            "name": "Ocean Gene Atlas",
            "description": "The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping sequence reads onto gene catalogs).\nUser queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive maps and plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.",
            "homepage": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/",
            "biotoolsID": "Ocean_Gene_Atlas",
            "biotoolsCURIE": "biotools:Ocean_Gene_Atlas",
            "tool_type": [
                "Database portal"
            ],
            "collection": [
                "elixir-fr-sdp-2019"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3941",
                "http://edamontology.org/topic_3387",
                "http://edamontology.org/topic_3174",
                "http://edamontology.org/topic_0610"
            ],
            "primary_publication": [
                "10.1093/nar/gky376"
            ],
            "operating_system": [],
            "tool_credit": [
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                    "type_role": [
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                    ],
                    "name": null,
                    "email": "oceangeneatlas@mio.osupytheas.fr",
                    "url": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/credits",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
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                    ],
                    "name": "MIO",
                    "email": null,
                    "url": "https://www.mio.osupytheas.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
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                    "type_role": [],
                    "name": "OCEANOMICS",
                    "email": null,
                    "url": "http://www.oceanomics.eu/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Funding agency",
                    "note": "ANR-11-BTBR-0008"
                }
            ],
            "tool_licence": "Not licensed",
            "documentation": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/build/pdf/Ocean-Gene-Atlas_User_Manual.pdf",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T20:59:34.208631Z",
            "teams": [],
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        },
        {
            "id": 293,
            "name": "madbot",
            "description": "madbot, developed by IFB, simplifies scientific data management and sharing. As research data grows, ensuring accessibility and reusability becomes complex.\nUnlike other tools, madbot automates data organization and description, saving time and ensuring consistency. It connects to repositories like Zenodo and ENA, enabling seamless submissions. Its user-friendly interface requires no technical skills, while its backend ensures data accuracy and high-quality metadata.\nWith an extensible architecture, madbot integrates with diverse storage systems and standards, adapting to researchers' needs. By streamlining data sharing, it promotes open science and global collaboration.",
            "homepage": "https://madbot.france-bioinformatique.fr",
            "biotoolsID": "madbot",
            "biotoolsCURIE": "biotools:madbot",
            "tool_type": [
                "Web API",
                "Web application"
            ],
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            "scientific_topics": [
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                "http://edamontology.org/topic_3572",
                "http://edamontology.org/topic_0219",
                "http://edamontology.org/topic_0091",
                "http://edamontology.org/topic_0089",
                "http://edamontology.org/topic_3345",
                "http://edamontology.org/topic_4012"
            ],
            "primary_publication": [],
            "operating_system": [
                "Mac",
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [],
                    "name": "IFB - Institut Français de Bioinformatique",
                    "email": null,
                    "url": "https://www.ifb-elixir.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
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                    ],
                    "name": "Julien Seiler",
                    "email": "julien.seiler@france-bioinformatique.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-4549-5188",
                    "gridid": null,
                    "typeEntity": "Person",
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                },
                {
                    "type_role": [
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                        "Developer"
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                    "name": "Thomas Denecker",
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                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-1421-7641",
                    "gridid": null,
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                        "Developer"
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                    "name": "Imane Messak",
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                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-1654-6652",
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