{"count":144,"next":"https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?limit=20&offset=20&ordering=-difficultyLevel","previous":null,"results":[{"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/"]},{"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 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Phinch","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html","fileName":"mothur-miseq-sop-short","topics":["http://edamontology.org/topic_3697","http://edamontology.org/topic_0637"],"keywords":["Galaxy","Metabarcoding"],"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/"]},{"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/"]},{"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/"]},{"id":140,"name":"TP Cluster","description":"TP for cluster training (bioinfo genotoul facility)","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://genotoul-bioinfo.pages.mia.inra.fr/linux-cluster/","fileName":"linux-cluster","topics":[],"keywords":["Cluster"],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"Novice","providedBy":[{"id":22,"name":"Genotoul-bioinfo","url":"https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/"}],"dateCreation":null,"dateUpdate":null,"licence":"CC BY-NC-SA","maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/300/"]},{"id":128,"name":"Mapping with Galaxy","description":"This tutorial covers the questions:\r\n- What is mapping?\r\n- What two things are crucial for a correct mapping?\r\n- What is BAM?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Define what mapping is\r\n- Perform mapping of reads on a reference genome\r\n- Evaluate the mapping output","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html","fileName":"mapping","topics":["http://edamontology.org/topic_0102"],"keywords":["Mapping"],"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/"]},{"id":130,"name":"Taxonomic Profiling and Visualization of Metagenomic Data","description":"This tutorial covers the questions:\r\n- Which species (or genera, families, …) are present in my sample?\r\n- What are the different approaches and tools to get the community profile of my sample?\r\n- How can we visualize and compare community profiles?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Explain what taxonomic assignment is\r\n- Explain how taxonomic assignment works\r\n- Apply Kraken and MetaPhlAn to assign taxonomic labels\r\n- Apply Krona and Pavian to visualize results of assignment and understand the output\r\n- Identify taxonomic classification tool that fits best depending on their data","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html","fileName":"taxonomic-profiling","topics":["http://edamontology.org/topic_3697","http://edamontology.org/topic_3174","http://edamontology.org/topic_0637"],"keywords":["Galaxy"],"audienceTypes":["Undergraduate","Graduate","Professional (initial)","Professional (continued)"],"audienceRoles":["Researchers","Life 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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/"]},{"id":142,"name":"Introduction to python","description":"Training slides (theory and exercises)","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://training-python-for-biology-genotoul-bioinfo-a77c191514cdd1dc1b.pages.mia.inra.fr/#/title-slide","fileName":"training-python-for-biology","topics":["http://edamontology.org/topic_3316"],"keywords":["Python Language"],"audienceTypes":["Professional (continued)"],"audienceRoles":["Life scientists"],"difficultyLevel":"Novice","providedBy":[{"id":22,"name":"Genotoul-bioinfo","url":"https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/"}],"dateCreation":null,"dateUpdate":null,"licence":"Creative Commons Attribution 4.0 International License","maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/300/"]},{"id":137,"name":"Linux slides","description":"Slides for linux session (genotoul bioinfo facility)","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://bioinfo.genotoul.fr/wp-content/uploads/Formation_LINUX_GenoToul_2024.pdf","fileName":"Formation_LINUX_GenoToul_2024.pdf","topics":[],"keywords":["Operating systems"],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"Novice","providedBy":[],"dateCreation":null,"dateUpdate":null,"licence":"CC BY-NC-SA","maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/300/"]},{"id":143,"name":"workflows nf-core","description":"Tutorial to launch and configure nf-core workflows on genotoul bioinfo cluster","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://genotoul-bioinfo.pages.mia.inra.fr/use-nextflow-nfcore-course/","fileName":"use-nextflow-nfcore-course","topics":["http://edamontology.org/topic_0769"],"keywords":["Nextflow"],"audienceTypes":["Professional (continued)"],"audienceRoles":["Life 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facility)","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://bioinfo.genotoul.fr/wp-content/uploads/Formation_cluster_SLURM_2024.pdf","fileName":"Formation_cluster_SLURM_2024.pdf","topics":[],"keywords":["Cluster"],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"Novice","providedBy":[{"id":22,"name":"Genotoul-bioinfo","url":"https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/"}],"dateCreation":null,"dateUpdate":null,"licence":"CC BY-NC-SA","maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/300/"]},{"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_3474","http://edamontology.org/topic_3316","http://edamontology.org/topic_3391","http://edamontology.org/topic_3365","http://edamontology.org/topic_0092","http://edamontology.org/topic_2269","http://edamontology.org/topic_3307","http://edamontology.org/topic_0091"],"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/"}],"dateCreation":null,"dateUpdate":null,"licence":null,"maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/762/"]},{"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/"]},{"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/"]},{"id":141,"name":"training material sed and awk training","description":"training material sed and awk training (genotoul bioinfo facility)","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://genoweb.toulouse.inra.fr/~klopp/SedAwk2024/Processing_large_files_with_sed_awk_2024.pdf","fileName":"Processing_large_files_with_sed_awk_2024.pdf","topics":["http://edamontology.org/topic_3316"],"keywords":["Programming Languages & Computer Sciences"],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"Intermediate","providedBy":[{"id":22,"name":"Genotoul-bioinfo","url":"https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/"}],"dateCreation":null,"dateUpdate":null,"licence":"Creative Commons Attribution 4.0 International License","maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/300/"]},{"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.","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://genotoul-bioinfo.pages.mia.inra.fr/training-rnaseq","fileName":"training-rnaseq","topics":[],"keywords":[],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"Intermediate","providedBy":[],"dateCreation":null,"dateUpdate":null,"licence":null,"maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/300/"]},{"id":136,"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.","communities":[],"elixirPlatforms":[],"doi":null,"fileLocation":"https://www.nathalievialaneix.eu/teaching/rnaseq.html","fileName":"rnaseq.html","topics":[],"keywords":[],"audienceTypes":[],"audienceRoles":[],"difficultyLevel":"Intermediate","providedBy":[],"dateCreation":null,"dateUpdate":null,"licence":null,"maintainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/300/"]}]}