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            "name": "training RNASeq biostat part",
            "description": "This course is part of the INRAE training session about “bioinformatics and biostatistics analysis of RNA-seq data” and of the Biostatistics platform “Initiation à LA statistique, niveau 4”. \r\nThe material provided on the present webpage is related to the biostatistics part and covers the following topics:\r\n\r\nR and RStudio\r\ndesign of experiments\r\nvariability\r\ncount data normalization\r\ndifferential analysis\r\nThe material has originally been prepared by Ignacio Gonzales, Annick Moisan and myself. The class has already been taught by these persons but also by Gaëlle Lefort and Jérôme Mariette.\r\n\r\nPre-requisites: A background in R programming is necessary for this class. Before the class, please download the course material and install R, RStudio and the packages as described below. To produce high quality figures, I will use ggplot2 for plots but will not enter into details about the ggplot2 syntax. If you are not familiar with it, you can just use these command lines or switch to base plots instead.",
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            "id": 135,
            "name": "training RNASEQ Bioinfo part",
            "description": "Cette formation a pour but de vous aider à traiter les séquences courtes issues des plates-formes de séquençage Illumina. Vous y découvrirez les formats de séquences et d’alignement les biais connus et mettrez en œuvre des logiciels d'alignement épissé sur génome de référence, la recherche de nouveaux gènes, de nouveaux transcrits et la quantification de l'expression de ces gènes et transcrits.",
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            "id": 125,
            "name": "ETBII 2023",
            "description": "All the training materials dedicated to the IFB's Integrative Bioinformatics Thematic School, which took place in January 2023.",
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            "fileLocation": "https://moodle.france-bioinformatique.fr/course/view.php?id=13",
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                "http://edamontology.org/topic_3316",
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                "Semantic web",
                "Data Integration"
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            "name": "Snakemake tutorial: Gene regulation",
            "description": "Workflow 1: Rules and targets\nWorkflow 2: Introducing wildcards\nWorkflow 3: Keywords\nWorkflow 4: Combining rules\nWorkflow 5: Configuration file\nWorkflow 6: Separated files\n",
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            "name": "IFB Cloud tutorial: Gene regulation",
            "description": "1. Using the Gene-regulation appliance\n1.1 Requirements\n1.2 Virtual disk creation\n1.3 Creation of an instance\n1.4 Connection to the device\n1.5 Download source data\n1.6 Execute workflow\n\n2. Visualizing results\n2.1 Install and run the X2Go client on your host computer\n2.2 Visualize results\nFastQC\nIGV\n\n\n3. Create your own Gene-regulation appliance\nCreation of an instance\nInstalling programs and dependencies\nGet the gene-regulation repository\nRun makefile to install the dependencies\n\n",
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                "Cloud Computing"
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            "id": 122,
            "name": "Docker tutorial: Gene regulation",
            "description": "Get started with Docker!\nCreate a Docker account\nInstall Docker on your local host\nCreate shared repositories and download source data\nFetch the Docker image and run it with shared folders\nExecute the pipeline\n\nJVH / Mac\n",
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            "name": "The IFB cloud for bioinformatics",
            "description": "\n\tPractical work to introduce basic and advanced usage of the IFB cloud\nHowto launch virtual machines\nManaging your data in the cloud ;\nHowto to connect to your VMS (SSH, web, remote desktop)\nPersonalizing your VMs (approver, galaxy, docker)\n\n",
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            "name": "Initiation to Galaxy",
            "description": "DNA-sequence analysis: from raw reads to variants calling within the galaxy environement.\n",
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            "doi": null,
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            "id": 119,
            "name": "Visualization of NGS data with IGV",
            "description": "Visualisation of next-gen sequencing data with Integrative Genomics Viewer\n",
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            "name": "Chip-seq: Introduction to the Workshop",
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            "name": "Chip-seq: Peak calling tutorial",
            "description": "The aim is to :\nUnderstand how to process reads to obtain peaks (peak-calling).\nBecome familiar with differential analysis of peaks\nIn practice :\nObtain dataset from GEO\nAnalyze mapped reads\nObtain set(s) of peaks, handle replicates\nDifferential analysis of peak\n",
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            "name": "Chip-seq: Functional Annotation tutorial",
            "description": "Global Objective\nGiven a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.\n",
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            "name": "Chip-seq: Pattern Analysis tutorial",
            "description": "Goal\nThe aim is to :\nGet familiar with motif analysis of ChIP-seq data.\nLearn de novo motif discovery methods.\nIn practice :\nMotif discovery with peak-motifs\nDifferential analysis\nRandom controls\n",
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            "name": "Chip Seq: Annotation and visualization Lesson",
            "description": "How to add biological meaning to peaks\n",
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            "name": "Chip Seq: Annotation and visualization Tutorial",
            "description": "Global Objective\nGiven a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.\n",
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            "name": "Chip-seq: Motif Analysis Tutorial",
            "description": "Introduction\nGoal\nThe aim is to :\nGet familiar with motif analysis of ChIP-seq data.\nLearn de novo motif discovery methods.\nIn practice :\nMotif discovery with peak-motifs\nDifferential analysis\nRandom controls\n",
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            "name": "Chip-seq: Discovering motifs in peaks with RSAT",
            "description": "Read mapping: from raw reads to aligned reads.\nPeak calling: from aligned reads to regions/peaks of high read density.\nChIP-seq annotation\nIdentification of genes related to the peaks.\nProfiles of ChIP-seq reads around reference points (TSS, histone marks,).\nFunctional enrichment of the genes related to the peaks.\n\n",
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            "name": "DNA-seq analysis: From raw reads to processed alignments",
            "description": "Objectives:\nMapping the DNA-seq data to the reference genome\nProcess the alignments for the variant calling\n",
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            "id": 63,
            "name": "Variant Filtering",
            "description": "Use cases:\nExtact a subset of variants\nCombine variants from several analysis\n\nCompare obtained variants from several data types\n\n\nIdentify new variants compare to a reference list\n\n\nApply specific filters for Chip Design\n\n",
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            "id": 109,
            "name": "RNA-Seq: Differential Expression Analysis",
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