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            "name": "TrEMOLO",
            "description": "Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.",
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            "biotoolsCURIE": "biotools:tremolo",
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                    "name": "Anna-Sophie Fiston-Lavier",
                    "email": "anna-sophie.fiston-lavier@umontpellier.fr",
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                    "name": "Séverine Chambeyron",
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                    "url": null,
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            "teams": [
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            "source_repository": "https://dataverse.ird.fr/dataverse/tremolo_data"
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            "id": 247,
            "name": "metagWGS",
            "description": "metagWGS is a workflow dedicated to the analysis of metagenomic data. It allows assembly, taxonomic annotation, and functional annotation of predicted genes. Since release 2.3, binning step with the possibility of cross-alignment is included. It has been developed in collaboration with several CATI BIOS4biol agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.",
            "homepage": "https://forgemia.inra.fr/genotoul-bioinfo/metagwgs",
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            "biotoolsCURIE": "biotools:metagwgs",
            "tool_type": [
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            "scientific_topics": [
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            "operating_system": [
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            "tool_credit": [
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                        "Primary contact"
                    ],
                    "name": "Claire Hoede",
                    "email": "claire.hoede@inrae.fr",
                    "url": null,
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            "documentation": "https://genotoul-bioinfo.pages-forge.inrae.fr/metagwgs/master/index.html",
            "maturity": "Mature",
            "cost": "Free of charge",
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            "citations": null,
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            "last_update": "2025-12-11T14:51:44.804907Z",
            "teams": [
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            ],
            "source_repository": "https://forge.inrae.fr/genotoul-bioinfo/metagwgs"
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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 API",
                "Web application"
            ],
            "collection": [
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                "http://edamontology.org/topic_0780",
                "http://edamontology.org/topic_0091",
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                "http://edamontology.org/topic_3071",
                "http://edamontology.org/topic_3810"
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            ],
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                        "Support"
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                    "name": "URGI support",
                    "email": "urgi-support@inrae.fr",
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            ],
            "tool_licence": "BSD-3-Clause",
            "documentation": "https://urgi.versailles.inrae.fr/faidare/help",
            "maturity": "Emerging",
            "cost": "Free of charge",
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            "citations": null,
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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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            "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",
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                "http://edamontology.org/topic_0634",
                "http://edamontology.org/topic_3673",
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            ],
            "primary_publication": [
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            ],
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                "Linux"
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                    "name": "IBENS - DYOGEN Team",
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                    "note": null
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                    "name": "Hugues Roest Crollius",
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                    "gridid": null,
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                    "name": "Lambert Moyon",
                    "email": "moyon@bio.ens.psl.eu",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-2390-3942",
                    "gridid": null,
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                    "name": "Alexandra Louis",
                    "email": "alexandra.louis@bio.ens.psl.eu",
                    "url": null,
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                    "gridid": null,
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                    "name": "Camille Berthelot",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-5054-2690",
                    "gridid": null,
                    "typeEntity": "Person",
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            "cost": "Free of charge",
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            "citations": null,
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            "last_update": "2024-11-24T14:55:59.341655Z",
            "teams": [
                "PB-IBENS"
            ],
            "source_repository": "https://github.com/DyogenIBENS/FINSURF/"
        },
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            "id": 286,
            "name": "pyBRAvo",
            "description": "From a list of genes, pyBRAvo produces upstream regulation or signaling networks. pyBRAvo internally leverages the BioPAX ontolgy, the PathwayCommons knowledge graph, and the SPARQL semantic web query language. pyBRAvo can be used through either a Jupyter notebook, or a command line interface.",
            "homepage": "https://github.com/pyBRAvo/pyBRAvo",
            "biotoolsID": "pybravo",
            "biotoolsCURIE": "biotools:pybravo",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0602",
                "http://edamontology.org/topic_2259"
            ],
            "primary_publication": [
                "10.1093/database/baaa113"
            ],
            "operating_system": [],
            "tool_credit": [
                {
                    "type_role": [
                        "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"
                    ],
                    "name": "Alban Gaignard",
                    "email": "alban.gaignard@univ-nantes.fr",
                    "url": "http://albangaignard.github.io/",
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                    "gridid": null,
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                },
                {
                    "type_role": [
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                    ],
                    "name": "Marie Lefebvre",
                    "email": "marie.lefebvre@inrae.fr",
                    "url": "https://mariebvr.github.io/marieBvr/",
                    "orcidid": "https://orcid.org/0000-0002-3093-5873",
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                    "name": "Maxime Folschette",
                    "email": "maxime.folschette@centralelille.fr",
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                    "name": "Jeremy Bourdon",
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                    "type_role": [],
                    "name": "Carito Guziolowski",
                    "email": null,
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                    "gridid": null,
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                    "name": "SyMeTRIC",
                    "email": null,
                    "url": "http://symetric.univ-nantes.fr/doku.php",
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                    "note": null
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            "documentation": "https://github.com/pyBRAvo/pyBRAvo",
            "maturity": "Mature",
            "cost": "Free of charge",
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            "citations": null,
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            "last_update": "2022-05-31T14:22:33.309326Z",
            "teams": [
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            ],
            "source_repository": "https://github.com/pyBRAvo/pyBRAvo"
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            "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": [
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            "scientific_topics": [
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                "http://edamontology.org/topic_3071"
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                "10.1186/s13742-016-0131-8"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
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                        "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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                    "note": null
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                    ],
                    "name": null,
                    "email": "gigwa@cirad.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
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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": [
                "South Green"
            ],
            "source_repository": "https://github.com/SouthGreenPlatform/Gigwa2"
        },
        {
            "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": [
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            ],
            "operating_system": [
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                "Windows",
                "Mac"
            ],
            "tool_credit": [
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                    "name": null,
                    "email": "plechat@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
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            ],
            "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": [
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            "source_repository": null
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        {
            "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": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Marie Touchon",
                    "email": "mtouchon@pasteur.fr",
                    "url": null,
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                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
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            ],
            "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": [
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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_0610",
                "http://edamontology.org/topic_3387",
                "http://edamontology.org/topic_3174",
                "http://edamontology.org/topic_3941"
            ],
            "primary_publication": [
                "10.1093/nar/gky376"
            ],
            "operating_system": [],
            "tool_credit": [
                {
                    "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"
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                    "name": null,
                    "email": "oceangeneatlas@mio.osupytheas.fr",
                    "url": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/credits",
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                    "gridid": null,
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            "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": 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"
            ],
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            "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"
            ],
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            "operating_system": [
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                "Linux",
                "Windows"
            ],
            "tool_credit": [
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                    "type_role": [
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                    ],
                    "name": "Mathieu Rouard",
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                "Database portal"
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                    "name": "BiRD bioinformatics facility",
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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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                "http://edamontology.org/topic_0196",
                "http://edamontology.org/topic_3174",
                "http://edamontology.org/topic_0769",
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}