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

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

Slides

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

FAQs

• Importing via links
• Copy a dataset between histories

GitHub Activity

github Issues Reported

14 Merged Pull Requests

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

• 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
• Metabolomics second try
  feature
  review-needed
  CoFest
  metabolomics
  new tutorial
• Small fix in conda slides

Reviewed 22 PRs

We love our community reviewing each other's work!

• 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
• De novo transcriptome assembly, annotation, and differential expression analysis
  work-in-progress
  transcriptomics
  new tutorial
  new contributor(s)

External Links

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