Training Material List
Handles creating, reading and updating training materials.
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This library can be a predicted TE library built by TEdenovo\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Annotation" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CeCILL", "maintainers": [] }, { "id": 101, "name": "REPET: TEdenovo tutorial", "description": "The TEdenovo pipeline follows a philosophy in three first steps:\nDetection of repeated sequences (potential TE)\nClustering of these sequences\nGeneration of consensus sequences for each cluster, representing the ancestral TE\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://urgi.versailles.inra.fr/Tools/REPET/TEdenovo-tuto", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Annotation" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CeCILL", "maintainers": [] }, { "id": 92, "name": "HOVERGEN tutorial", "description": "HOVERGEN is a database containing homologous vertebrate protein and nucleotide sequences. It allows to easily select similar gene sequences from a wide range of vertebrates. Hence it becomes particularly useful in comparative genomics, phylogeny and evolutionary studies on a molecular level. HOVERGEN Clean contains only complete sequences which reattach to their family. Hence its library is smaller, but more reliable.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.prabi.fr/spip.php?article58", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "proteomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [ { "id": 19, "name": "PRABI-AMSB", "url": "https://catalogue.france-bioinformatique.fr/api/team/PRABI-AMSB/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 94, "name": "Searching for sequence: Tutorial", "description": "Quick Search is dedicated to a quick search for sequences or sequence families in the databases available on the PBIL server. It is an alternative to WWW Query which allows more complex queries. Quick Search allows you to retrieve sequences or sequence families associated to a single word without specifying what is this word. You can enter indifferently a keyword, a sequence name or accession number, or a taxa name.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.prabi.fr/spip.php?article17", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Pattern recognition" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/715/?format=api" ] }, { "id": 104, "name": "Exploring microbiomes with the MicroScope Platform", "description": "This module is separated in different courses:\nMicroScope: General overview, Keyword search and gene cart functionalities\n\n\n\n\n\n\n\n\n\n\n\n\nFunctional annotation of microbial genomes\n\n\n\n\n\n\n\n\nFunctional annotation of microbial genomes: Prediction of enzymatic functions\n\n\n\n\n\n\n\n\nRelational annotation of bacterial genomes: synteny\n\n\n\n\n\n\n\n\nAutomatic functional assignation and expert annotation of genes\n\n\n\n\n\n\n\n\nRelational annotation of bacterial genomes: phylogenetic profiles\n\n\n\n\n\n\n\n\nRelational annotation of bacterial genomes: pan-genome analysis\n\n\n\n\n\n\n\n\nRelational annotation of bacterial genomes: metabolic pathways\n\n\n\n\nSyntactic re-annotation of public microbial genomes\n\n\n\n\nSyntactic annotation of microbial genomes\n\n\n\n\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/Cours_MicroScope_mars2016_18-125.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Annotation", "Transcriptomics", "Microbial evolution", "Metabolomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-03-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/718/?format=api" ] }, { "id": 105, "name": "Exploring Microscope Platform", "description": "\n \n\nHow to use the Microscope Platform to annotate and analyze microbial genomes.\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/Cours_MicroScope_mars2016_1-17.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Annotation", "Sequence analysis", "Transcriptomics", "Microbial evolution", "Metabolomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-03-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/718/?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": 110, "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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/elodie_girard-itmo2015_mapping_preprocess.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Variant calling", "Alignment", "DNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/256/?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": 93, "name": "Cross Taxa Tutorial", "description": "How query databases according to complex taxonomic critera\nCross-Taxa allows to retrieve gene families that are shared by a given set of taxa, or which are specific to a set of taxa. It is also possible to select genes families which are associated to a certain set of taxa but which are not found in a second set of taxa. Any taxonomic level can be used.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.prabi.fr/spip.php?article41", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/715/?format=api" ] }, { "id": 60, "name": "Differential analysis of RNA-Seq data", "description": "Design, describe, explore and model\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/R02-R03_slidesRoscoff_stats_HVaret.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/371/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/626/?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": 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": 65, "name": "Chip-seq Analysis", "description": "Quality, normalisation and peak calling\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/C01_ChIP_SEQ_EBA_2016-11-22.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Chip-Seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-22", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/695/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/696/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/697/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/698/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?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": 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" ] } ] }