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            "name": "Galaxy France",
            "description": "Galaxy is an open-source platform for FAIR data analysis that enables users to: i) use tools from various domains (that can be plugged into workflows) through its graphical web interface, ii) run code in interactive environments (RStudio, Jupyter, ...) along with other tools or workflows, iii) manage data by sharing and publishing results, workflows, and visualizations, iv) ensure reproducibility by capturing the necessary information to repeat and understand data analyses.\n\nUseGalaxy.fr is the national Galaxy instance for ELIXIR-FR.",
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                    "name": "IFB - Institut Français de Bioinformatique",
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            "biotoolsID": "finsurf",
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                "http://edamontology.org/topic_3673",
                "http://edamontology.org/topic_0634",
                "http://edamontology.org/topic_0749"
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            "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",
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                "http://edamontology.org/topic_0089"
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            "teams": [
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                "IFB Core"
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            "name": "ChagasDB",
            "description": "Manual-curated database regrouping published results referenced in Pubmed.",
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                    "name": "Edecio Cunha-Neto",
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                    "name": "Christophe Chevillard",
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            "last_update": "2024-11-24T14:25:34.821693Z",
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            "name": "AgroLD",
            "description": "The RDF Knowledge-based Database for plant molecular networks.",
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            "last_update": "2019-11-05T14:52:28Z",
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            "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": [
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            "scientific_topics": [
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            ],
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                    "name": "Dimitri MEISTERMANN",
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                    "name": "BiRD bioinformatics facility",
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                    "url": "https://pf-bird.univ-nantes.fr",
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                    "name": "Eric Charpentier",
                    "email": "eric.charpentier@univ-nantes.fr",
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                    "orcidid": "https://orcid.org/0000-0002-8571-7603",
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                    "name": "Broad Institute",
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                    "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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                    "name": "Solenne Dumont",
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