Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=120&ordering=-topics
{ "count": 149, "next": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=140&ordering=-topics", "previous": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=100&ordering=-topics", "results": [ { "id": 126, "name": "Galaxy 101 for everyone", "description": "This practical aims at familiarizing you with the Galaxy user interface. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows and sharing your work. Not everyone has the same background and that’s ok!", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html", "fileName": "galaxy-intro-101-everyone", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 67, "name": "Galaxy: Initiation II", "description": "Galaxy II: common tools, quality control; alignment; data managment\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/G045_16-11-21-galaxy-tp-initiation-II-0.3.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-21", "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/362/?format=api" ] }, { "id": 50, "name": "Welcome and Introduction", "description": "\n \n\nIntroduction message of the EGDW 2017\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://ressources.france-bioinformatique.fr/sites/default/files/introduction.pdf", "fileName": " introduction.pdf", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-16", "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 51, "name": "Eukaryotic small RNA", "description": "\n \n\nSmall RNAseq data analysis for miRNA identification\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/sRNA-Seq.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/642/?format=api" ] }, { "id": 76, "name": " Reconstructing genomes from metagenomes: The holy grail of microbiology", "description": "Shotgun metagenomics provides insights into a larger context of naturally occurring microbial genomes when short reads are assembled into contiguous DNA segments (contigs). Contigs are often orders of magnitude longer than individual sequences, offering improved annotations, and key information about the organization of genes in cognate genomes. Several factors affect the assembly performance, and the feasibility of the assembly-based approaches varies across environments. However, increasing read lengths, novel experimental approaches, advances in computational tools and resources, and improvements in assembly algorithms and pipelines render the assembly-based metagenomic workflow more and more accessible. The utility of metagenomic assembly remarkably increases when contigs are organized into metagenome-assembled genomes (MAGs). Often-novel MAGs frequently provide deeper insights into bacterial lifestyles that would otherwise remain unknown as evidenced by recent discoveries. The increasing rate of the recovery of MAGs presents new opportunities to link environmental distribution patterns of microbial populations and their functional potential, and transforms the field of microbiology by providing a more complete understanding of the microbial life, ecology, and evolution.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_5/Reconstructing_genomes_from_metagenomes_the_holy_grail_of_microbiology/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-12-16", "dateUpdate": null, "licence": "CC BY-NC-ND", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/665/?format=api" ] }, { "id": 69, "name": "New perspectives on nitrite-oxidizing bacteria - linking genomes to physiology", "description": "It is a generally accepted characteristic of the biogeochemical nitrogen cycle that nitrification is catalyzed by two distinct clades of microorganisms. First, ammonia-oxidizing bacteria and archaea convert ammonia to nitrite, which subsequently is oxidized to nitrate by nitrite-oxidizing bacteria (NOB). The latter were traditionally perceived as physiologically restricted organisms and were less intensively studied than other nitrogen-cycling microorganisms. This picture is contrasted by new discoveries of an unexpected high diversity of mostly uncultured NOB and a great physiological versatility, which includes complex microbe-microbe interactions and lifestyles outside the nitrogen cycle. Most surprisingly, close relatives to NOB perform complete nitrification (ammonia oxidation to nitrate), a process that had been postulated to occur under conditions selecting for low growth rates but high growth yields.\nThe existence of Nitrospira species that encode all genes required for ammonia and nitrite oxidation was first detected by metagenomic analyses of an enrichment culture for nitrogen-transforming microorganisms sampled from the anoxic compartment of a recirculating aquaculture system biofilter. Batch incubations and FISH-MAR experiments showed that these Nitrospira indeed formed nitrate from the aerobic oxidation of ammonia, and used the energy derived from complete nitrification for carbon fixation, thus proving that they indeed represented the long-sought-after comammox organisms. Their ammonia monooxygenase (AMO) enzymes were distinct from canonical AMOs, therefore rendering recent horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. Instead, their AMO displayed highest similarities to the “unusual” particulate methane monooxygenase from Crenothrix polyspora, thus shedding new light onto the function of this sequence group. This recognition of a novel AMO type indicates that a whole group of ammonia-oxidizing microorganisms has been overlooked, and will improve our understanding of the environmental abundance and distribution of this functional group. Data mining of publicly available metagenomes already indicated a widespread occurrence in natural and engineered environments like aquifers and paddy soils, and drinking and wastewater treatment systems.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_8/New_perspectives_on_nitrite_xidizing_bacteria/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-12-16", "dateUpdate": null, "licence": "CC BY-NC-ND", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/700/?format=api" ] }, { "id": 81, "name": "Assessing microbial biogeography by using a metagenomic approach", "description": "Soils are highly complex ecosystems and are considered as one of the Earth’s main reservoirs of biological diversity. Bacteria account for a major part of this biodiversity, and it is now clear that such microorganisms have a key role in soil functioning processes. However, environmental factors regulating the diversity of below-ground bacteria still need to be investigated, which limits our understanding of the distribution of such bacteria at various spatial scales. The overall objectives of this study were: (i) to determine the spatial patterning of bacterial community diversity in soils at a broad scale, and (ii) to rank the environmental filters most influencing this distribution.\nThis study was performed at the scale of the France by using the French Soil Quality Monitoring Network. This network includes more than 2,200 soil samples along a systematic grid sampling. For each soil, bacterial diversity was characterized using a pyrosequencing approach targeting the 16S rRNA genes directly amplified from soil DNA, obtaining more than 18 million of high-quality sequences.\nThis study provides the first estimates of microbial diversity at the scale of France, with for example, bacterial richness ranging from 555 to 2,007 OTUs (on average: 1,289 OTUs). It also provides the first extensive map of bacterial diversity, as well as of major bacterial taxa, revealing a bacterial heterogeneous and spatially structured distribution at the scale of France. The main factors driving bacterial community distribution are the soil physico-chemical properties (pH, texture...) and land use (forest, grassland, crop system...), evidencing that bacterial spatial distribution at a broad scale depends on local filters such as soil characteristics and land use when regarding the community (quality, composition) as a whole. Moreover, this study also offers a better evaluation of the impact of land uses on soil microbial diversity and taxa, with consequences in terms of sustainability for agricultural systems.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_4/Assessing_microbial_biogeography_by_using_a_metagenomic_approach/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-12-16", "dateUpdate": null, "licence": "CC BY-NC-ND", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/709/?format=api" ] }, { "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.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://moodle.france-bioinformatique.fr/course/view.php?id=13", "fileName": "ETBII 2023 Training materials", "topics": [ "http://edamontology.org/topic_3316", "http://edamontology.org/topic_3474", "http://edamontology.org/topic_3391", "http://edamontology.org/topic_3365", "http://edamontology.org/topic_0092", "http://edamontology.org/topic_2269", "http://edamontology.org/topic_0091", "http://edamontology.org/topic_3307" ], "keywords": [ "Biological network inference and analysis", "Multivariate analyses", "Semantic web", "Data Integration" ], "audienceTypes": [ "Professional (initial)" ], "audienceRoles": [ "Life scientists", "Computer scientists", "Bioinformaticians" ], "difficultyLevel": "Novice", "providedBy": [ { "id": 29, "name": "IFB Core", "url": "https://catalogue.france-bioinformatique.fr/api/team/IFB%20Core/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/762/?format=api" ] }, { "id": 144, "name": "Reference-based RNA-Seq data analysis with Galaxy", "description": "This tutorial covers the questions:\r\n- What are the steps to process RNA-Seq data?\r\n- How to identify differentially expressed genes across multiple experimental conditions?\r\n- What are the biological functions impacted by the differential expression of genes?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Check a sequence quality report generated by FastQC for RNA-Seq data\r\n- Explain the principle and specificity of mapping of RNA-Seq data to an eukaryotic reference genome\r\n- Select and run a state of the art mapping tool for RNA-Seq data\r\n- Evaluate the quality of mapping results\r\n- Describe the process to estimate the library strandness\r\n- Estimate the number of reads per genes\r\n- Explain the count normalization to perform before sample comparison\r\n- Construct and run a differential gene expression analysis\r\n- Analyze the DESeq2 output to identify, annotate and visualize differentially expressed genes\r\n- Perform a gene ontology enrichment analysis\r\n- Perform and visualize an enrichment analysis for KEGG pathways", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html", "fileName": "rna-seq", "topics": [ "http://edamontology.org/topic_0102", "http://edamontology.org/topic_1775", "http://edamontology.org/topic_0203", "http://edamontology.org/topic_3308", "http://edamontology.org/topic_3170" ], "keywords": [ "Galaxy", "RNA-seq" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 132, "name": "Metatranscriptomics analysis using microbiome RNA-seq data", "description": "This tutorial covers the questions:\r\n- How to analyze metatranscriptomics data?\r\n- What information can be extracted of metatranscriptomics data?\r\n- How to assign taxa and function to the identified sequences?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Choose the best approach to analyze metatranscriptomics data\r\n- Understand the functional microbiome characterization using metatranscriptomic results\r\n- Understand where metatranscriptomics fits in ‘multi-omic’ analysis of microbiomes\r\n- Visualise a community structure", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics/tutorial.html", "fileName": "metatranscriptomics", "topics": [ "http://edamontology.org/topic_1775", "http://edamontology.org/topic_3941" ], "keywords": [ "Galaxy" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "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.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://moodle.france-bioinformatique.fr/course/view.php?id=13", "fileName": "ETBII 2023 Training materials", "topics": [ "http://edamontology.org/topic_3316", "http://edamontology.org/topic_3474", "http://edamontology.org/topic_3391", "http://edamontology.org/topic_3365", "http://edamontology.org/topic_0092", "http://edamontology.org/topic_2269", "http://edamontology.org/topic_0091", "http://edamontology.org/topic_3307" ], "keywords": [ "Biological network inference and analysis", "Multivariate analyses", "Semantic web", "Data Integration" ], "audienceTypes": [ "Professional (initial)" ], "audienceRoles": [ "Life scientists", "Computer scientists", "Bioinformaticians" ], "difficultyLevel": "Novice", "providedBy": [ { "id": 29, "name": "IFB Core", "url": "https://catalogue.france-bioinformatique.fr/api/team/IFB%20Core/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/762/?format=api" ] }, { "id": 127, "name": "Quality Control with Galaxy", "description": "This tutorial covers the questions:\r\n- How to perform quality control of NGS raw data?\r\n- What are the quality parameters to check for a dataset?\r\n- How to improve the quality of a dataset?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC\r\n- Assess long reads FASTQ quality using Nanoplot and PycoQC\r\n- Perform quality correction with Cutadapt (short reads)\r\n- Summarise quality metrics MultiQC\r\n- Process single-end and paired-end data", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html", "fileName": "quality-control", "topics": [ "http://edamontology.org/topic_3168", "http://edamontology.org/topic_0091" ], "keywords": [ "Quality Control" ], "audienceTypes": [ "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 129, "name": "Bacterial Genome Annotation", "description": "This tutorial covers the questions:\r\n- Which genes are on a draft bacterial genome?\r\n- Which other genomic components can be found on a draft bacterial genome?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Run a series of tools to annotate a draft bacterial genome for different types of genomic components\r\n- Evaluate the annotation\r\n- Process the outputs to format them for visualization needs\r\n- Visualize a draft bacterial genome and its annotations", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html", "fileName": "bacterial-genome-annotation", "topics": [ "http://edamontology.org/topic_3301", "http://edamontology.org/topic_0219" ], "keywords": [ "Bacterial isolate", "Annotation", "Galaxy" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 129, "name": "Bacterial Genome Annotation", "description": "This tutorial covers the questions:\r\n- Which genes are on a draft bacterial genome?\r\n- Which other genomic components can be found on a draft bacterial genome?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Run a series of tools to annotate a draft bacterial genome for different types of genomic components\r\n- Evaluate the annotation\r\n- Process the outputs to format them for visualization needs\r\n- Visualize a draft bacterial genome and its annotations", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html", "fileName": "bacterial-genome-annotation", "topics": [ "http://edamontology.org/topic_3301", "http://edamontology.org/topic_0219" ], "keywords": [ "Bacterial isolate", "Annotation", "Galaxy" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "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.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://moodle.france-bioinformatique.fr/course/view.php?id=13", "fileName": "ETBII 2023 Training materials", "topics": [ "http://edamontology.org/topic_3316", "http://edamontology.org/topic_3474", "http://edamontology.org/topic_3391", "http://edamontology.org/topic_3365", "http://edamontology.org/topic_0092", "http://edamontology.org/topic_2269", "http://edamontology.org/topic_0091", "http://edamontology.org/topic_3307" ], "keywords": [ "Biological network inference and analysis", "Multivariate analyses", "Semantic web", "Data Integration" ], "audienceTypes": [ "Professional (initial)" ], "audienceRoles": [ "Life scientists", "Computer scientists", "Bioinformaticians" ], "difficultyLevel": "Novice", "providedBy": [ { "id": 29, "name": "IFB Core", "url": "https://catalogue.france-bioinformatique.fr/api/team/IFB%20Core/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/762/?format=api" ] }, { "id": 150, "name": "Plant Data Managment for Phenotyping Experiments - MIAPPE", "description": "The Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org) has been designed by ELIXIR, EMPHASIS and Bioversity international, to guide plant scientist in the management of experimental data. Furthermore, since genetic studies relies on the integration and the linking between phenotype and genotype datasets, relevant section of MIAPPE are beginning to be used for genotyping standards. This Webinar will give an overview of the current practices and methods for plant phenotyping data standardization, and how to deal with the variability and heterogeneity inherent to research and breeding data sets. Data management approaches at some of the major research organizations will be given as examples.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://hal.inrae.fr/hal-03102944", "fileName": "2020-12-MIAPPE-Webinar.pdf", "topics": [ "http://edamontology.org/topic_0625" ], "keywords": [ "Données" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-SA 4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/441/?format=api" ] }, { "id": 134, "name": "Nucleoli segmentation and feature extraction using CellProfiler", "description": "This tutorial covers the following questions:\r\n- How do I run an image analysis pipeline on public data using CellProfiler?\r\n- How do I analyse the DNA channel of fluorescence siRNA screens?\r\n- How do I download public image data into my history?\r\n- How do I segment and label cell nuclei?\r\n- How do I segment nucleoli (as the absence of DNA)?\r\n- How do I combine nuclei and nucleoli into one segmentation mask?\r\n- How do I extract the background of an image?\r\n- How do I relate the nucleoli to their parent nucleus?\r\n- How do I measure the image and object features?\r\n- How do I measure the image quality?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- How to download images from a public image repository.\r\n- How to segment cell nuclei using CellProfiler in Galaxy.\r\n- How to segment cell nucleoli using CellProfiler in Galaxy.\r\n- How to extract features for images, nuclei and nucleoli.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/tutorial-CP/tutorial.html", "fileName": "tutorial-CP", "topics": [ "http://edamontology.org/topic_3383", "http://edamontology.org/topic_3382" ], "keywords": [ "Galaxy" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 133, "name": "Introduction to image analysis using Galaxy", "description": "This tutorial covers the questions:\r\n- How do I use Galaxy with imaging data?\r\n- How do I convert images using Galaxy?\r\n- How do I display images in Galaxy?\r\n- How do I filter images in Galaxy?\r\n- How do I segment simple images in Galaxy?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- How to handle images in Galaxy.\r\n- How to perform basic image processing in Galaxy.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html", "fileName": "imaging-introduction", "topics": [ "http://edamontology.org/topic_3383", "http://edamontology.org/topic_3382" ], "keywords": [ "Galaxy" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 145, "name": "Introduction to Transcriptomics", "description": "This slidedecks presents the concepts behind transcriptomics", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/introduction/slides.html", "fileName": "transcriptomics-introduction", "topics": [ "http://edamontology.org/topic_0203", "http://edamontology.org/topic_3308", "http://edamontology.org/topic_3170" ], "keywords": [ "RNA-seq", "Transcriptomics (RNA-seq)" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 144, "name": "Reference-based RNA-Seq data analysis with Galaxy", "description": "This tutorial covers the questions:\r\n- What are the steps to process RNA-Seq data?\r\n- How to identify differentially expressed genes across multiple experimental conditions?\r\n- What are the biological functions impacted by the differential expression of genes?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Check a sequence quality report generated by FastQC for RNA-Seq data\r\n- Explain the principle and specificity of mapping of RNA-Seq data to an eukaryotic reference genome\r\n- Select and run a state of the art mapping tool for RNA-Seq data\r\n- Evaluate the quality of mapping results\r\n- Describe the process to estimate the library strandness\r\n- Estimate the number of reads per genes\r\n- Explain the count normalization to perform before sample comparison\r\n- Construct and run a differential gene expression analysis\r\n- Analyze the DESeq2 output to identify, annotate and visualize differentially expressed genes\r\n- Perform a gene ontology enrichment analysis\r\n- Perform and visualize an enrichment analysis for KEGG pathways", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html", "fileName": "rna-seq", "topics": [ "http://edamontology.org/topic_0102", "http://edamontology.org/topic_1775", "http://edamontology.org/topic_0203", "http://edamontology.org/topic_3308", "http://edamontology.org/topic_3170" ], "keywords": [ "Galaxy", "RNA-seq" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] } ] }