Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=100&ordering=-fileName
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All genomic coordinates correspond to the 2009 build of the reference human genome (hg19 / GRC37).\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/CNV_TD_guidelines_BJ.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Structural genomics", "Copy number" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 107, "name": "Genomic copy number Analysis", "description": "No description available\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/CNV_ROSCOFF_2015_BJ_20150930.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Structural genomics", "Copy number" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2015-09-10", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/318/?format=api" ] }, { "id": 108, "name": "RNA-Seq: isoform detection and quantification", "description": "transcriptome from new condition\ntissue-speci c transcriptome\ndifferent development stages\ntranscriptome from non model organism\ncancer cell\nRNA maturation mutant\n \nHow to manage RNA-Seq data with genes subjected to di erential\nsplicing?\nIs it possible to discover new isoforms?\nIs it possible to quantify abundance of each isoform\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/toffano-TP_RNASeq_Isoform.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Isoforms", "RNA-seq", "Transcriptomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/159/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/605/?format=api" ] }, { "id": 109, "name": "RNA-Seq: Differential Expression Analysis", "description": "\n \n\nBe careful about experimental design : avoid putting all the\nreplicates in the same lane, using the same barcode for the\nreplicates, putting different number of samples in lanes etc...\nNon- uniformity of the per base read distribution (Illumina Random\nHexamer Priming bias visible on the 13 first bases)\nBias hierarchy : biological condition >> concentration > run/flowcell> lane\nAt equivalent expression level, a long gene will have more reads than a short one.\nNon random coverage along the transcript.\nMultiple hit for some reads alignments.\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://ressources.france-bioinformatique.fr/sites/default/files/EBA/V4-2015/RNAseq/billerey-roscoff_expr_diff_tp-vfinal.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Differential Expression", "RNA-seq", "Transcriptomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/55/?format=api" ] }, { "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/FiltrageVariantNLapaluRoscoff2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Variant calling", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/694/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/719/?format=api" ] }, { "id": 111, "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/ChIP-seq_motifs_EBA2015_JvH.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Motif analysis", "Chip Seq", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api" ] }, { "id": 112, "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/tutorial/04_motif/motif_tutorial.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Pattern recognition", "Motif analysis", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 113, "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/tutorial/02_annotation/annotation.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Data visualization", "Annotation", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/698/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/644/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/720/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?format=api" ] }, { "id": 114, "name": "Chip Seq: Annotation and visualization Lesson", "description": "How to add biological meaning to peaks\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/slides/ChIP-seq_annotation_MD_2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Data visualization", "Annotation", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/698/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/644/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/720/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?format=api" ] }, { "id": 115, "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/tutorial/04_motif/motif_tutorial.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Pattern recognition", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/698/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/644/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/721/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?format=api" ] }, { "id": 116, "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/tutorial/02_annotation/annotation.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Functional Annotation", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 117, "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/tutorial/01_peak_calling/peak_calling_tutorial.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Peak calling", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/698/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/644/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/721/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?format=api" ] }, { "id": 118, "name": "Chip-seq: Introduction to the Workshop", "description": "Data visualization, quality control, normalization & peak calling\nPeak annotation\nFrom peaks to motifs\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/slides/chipseq_CarlHerrmann_Roscoff2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/661/?format=api" ] }, { "id": 119, "name": "Visualization of NGS data with IGV", "description": "Visualisation of next-gen sequencing data with Integrative Genomics Viewer\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/IGV-Roscoff-Septembre2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Data visualization", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 120, "name": "Initiation to Galaxy", "description": "DNA-sequence analysis: from raw reads to variants calling within the galaxy environement.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/GALAXY-TP-INITIATION-Roscoff-Septembre2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "DNA Analysis", "Variant calling", "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 121, "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://github.com/ekorpela/cloud-vm-workshop/blob/master/materials/IFBcloud/IFB%20cloud%20training%20ELIX-FI.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Cloud Computing", "Virtual machine" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-06-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/59/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/187/?format=api" ] }, { "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://github.com/rioualen/gene-regulation/blob/master/doc/gene-regulation_tutorials/gene-regulation_with_docker.Rmd", "fileName": "missing.txt", "topics": [], "keywords": [ "Gene regulation", "Docker" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-05-31", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/660/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api" ] }, { "id": 123, "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://github.com/rioualen/gene-regulation/blob/master/doc/gene-regulation_tutorials/gene-regulation_with_IFB_cloud.Rmd", "fileName": "missing.txt", "topics": [], "keywords": [ "Gene regulation", "Cloud Computing" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-05-31", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/660/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api" ] }, { "id": 124, "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://gene-regulation.readthedocs.io/en/latest/snakemake.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Gene regulation", "Snakemake" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-04-13", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/660/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api" ] } ] }