Gildas Le Corguillé

Affiliations

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

Editorial Roles

This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.

• Topic: Development in Galaxy
• Topic: Metabolomics

Tutorials

• Variant Analysis / Calling variants in non-diploid systems 🧐
• Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease 🧐
• Genome Annotation / Genome Annotation 🧐
• Genome Annotation / Genome annotation with Maker 🧐
• Assembly / Unicycler Assembly 🧐
• Assembly / De Bruijn Graph Assembly 🧐
• Statistics and machine learning / Basics of machine learning 🧐
• Statistics and machine learning / Interval-Wise Testing for omics data 🧐
• Transcriptomics / 1: RNA-Seq reads to counts 🧐
• Transcriptomics / De novo transcriptome assembly, annotation, and differential expression analysis ✍️ 🧐
• Transcriptomics / GO Enrichment Analysis 🧐
• Transcriptomics / De novo transcriptome reconstruction with RNA-Seq 🧐
• Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection 🧐
• Transcriptomics / Differential abundance testing of small RNAs 🧐
• Using Galaxy and Managing your Data / Name tags for following complex histories 🧐
• Using Galaxy and Managing your Data / Extracting Workflows from Histories 🧐
• Using Galaxy and Managing your Data / Rule Based Uploader: Advanced 🧐
• Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy Workflows 🧐
• Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line ✍️ 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for genomics 🧐
• Introduction to Galaxy Analyses / From peaks to genes 🧐
• Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy 🧐
• Development in Galaxy / Generic plugins 🧐
• Development in Galaxy / Contributing to BioBlend as a developer 🧐
• Development in Galaxy / JavaScript plugins 🧐
• Development in Galaxy / ToolFactory: Generating Tools From Simple Scripts 🧐
• Development in Galaxy / Creating Galaxy tools from Conda Through Deployment 🧐
• Development in Galaxy / ToolFactory: Generating Tools From More Complex Scripts 🧐
• Development in Galaxy / Data source integration 🧐
• Development in Galaxy / Galaxy Webhooks 🧐
• Metabolomics / Mass spectrometry: LC-MS preprocessing with XCMS ✍️ 🧐
• Metabolomics / Mass spectrometry: LC-MS analysis ✍️ 🧐
• Microbiome / Analyses of metagenomics data - The global picture 🧐
• Teaching and Hosting Galaxy training / Set up a Galaxy for Training 🧐
• Galaxy Server administration / Galaxy Installation with Ansible 📝
• Ecology / RAD-Seq to construct genetic maps 🧐
• Ecology / Species distribution modeling 🧐
• Ecology / RAD-Seq de-novo data analysis 🧐
• Ecology / Regional GAM 🧐
• Contributing to the Galaxy Training Material / Creating a new tutorial 🧐
• Contributing to the Galaxy Training Material / Including a new topic 🧐
• Epigenetics / ATAC-Seq data analysis 🧐
• Epigenetics / DNA Methylation data analysis 🧐
• Epigenetics / Formation of the Super-Structures on the Inactive X 🧐
• Computational chemistry / Setting up molecular systems 🧐
• Computational chemistry / Running molecular dynamics simulations using GROMACS 🧐
• Computational chemistry / Analysis of molecular dynamics simulations 🧐
• Single Cell / Pre-processing of Single-Cell RNA Data 🧐
• Single Cell / Single-cell quality control with scater 🧐

Slides

• Development in Galaxy / Galaxy from a developer point of view 🧐
• Development in Galaxy / Tool Shed: sharing Galaxy tools 🧐
• Development in Galaxy / Scripting Galaxy using the API and BioBlend 🧐
• Development in Galaxy / Prerequisites for building software/conda packages 🧐
• Development in Galaxy / Generic plugins 🧐
• Development in Galaxy / Tool development and integration into Galaxy ✍️ 🧐
• Development in Galaxy / Tool Dependencies and Containers 🧐
• Development in Galaxy / Tool Dependencies and Conda 🧐
• Development in Galaxy / Galaxy Interactive Environments 🧐
• Development in Galaxy / Galaxy Code Architecture 🧐
• Development in Galaxy / Galaxy Interactive Tours 🧐
• Development in Galaxy / Galaxy Webhooks 🧐
• Metabolomics / Introduction to Metabolomics ✍️ 🧐
• Metabolomics / Mass spectrometry: LC-MS preprocessing - advanced 🧐

FAQs

• Importing via links
• Copy a dataset between histories
• Downloading workflows
• Get the workflow id

Events

• Galaxy Beyond Basics: Mastering Workflows, Automation, and Scalability 🎪 🧑‍🏫

GitHub Activity

github Issues Reported

16 Merged Pull Requests

See all of the github Pull Requests and github Commits by Gildas Le Corguillé.

• workflow-automation - Add workflow dataset renaming
  review-needed
  galaxy-interface
• Add a tutorial about Planemo run but from the workflow creation
  review-needed
  template-and-tools
  galaxy-interface
  faqs
• De novo transcriptome reconstruction - some fix
  bug
  transcriptomics
• metabolomics - lcms - tutorial
  review-needed
  metabolomics
  new tutorial
  GCC
• admin - remove extra galaxy_file_path line
  admin

Reviewed 23 PRs

We love our community reviewing each other's work!

• Add a tutorial about Planemo run but from the workflow creation
  review-needed
  template-and-tools
  galaxy-interface
  faqs
• Add biotools recommendation to tool-from-scratch tutorial
• Split up and reorganise dev tutorials
• Remove duplicate snippets for building list collections
• Metabolomics > Lcms analysis : update
  review-needed
  metabolomics

External Links

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