Lucille Delisle

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: Epigenetics

Tutorials

• Contributing to the Galaxy Training Material / Updating diffs in admin training 🧐
• Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
• Contributing to the Galaxy Training Material / Creating a new tutorial ✍️
• Epigenetics / CUT&RUN data analysis 📝 🧐
• Epigenetics / ATAC-Seq data analysis ✍️ 🧐
• Single Cell / Understanding Barcodes 🧐
• Transcriptomics / Genome-wide alternative splicing analysis ✍️ 🧐
• Transcriptomics / RNA-seq Alignment with STAR 🧐
• Transcriptomics / Reference-based RNA-Seq data analysis ✍️ 🧐
• Transcriptomics / Network analysis with Heinz 🧐
• Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection 🧐
• Using Galaxy and Managing your Data / Group tags for complex experimental designs 🧐
• Using Galaxy and Managing your Data / Understanding Galaxy history system 🧐
• Proteomics / metaQuantome 1: Data creation 🧐
• Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters 🧐
• Galaxy Server administration / Enable upload via FTP ✍️ 🧐
• Galaxy Server administration / Reference Data with CVMFS 🧐
• Galaxy Server administration / Galaxy Installation with Ansible 📝 🧐
• Galaxy Server administration / Training Infrastructure as a Service (TIaaS) 🧐
• Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🧐
• Galaxy Server administration / Reference Data with CVMFS without Ansible 🧐
• Galaxy Server administration / Galaxy Monitoring with gxadmin 🧐
• Galaxy Server administration / Data Libraries 🧐
• Galaxy Server administration / Deploying Wireguard for private mesh networking 🧐
• Galaxy Server administration / Connecting Galaxy to a compute cluster 🧐
• Galaxy Server administration / Galaxy Monitoring with Reports 🧐
• Galaxy Server administration / Automation with Jenkins 🧐
• Galaxy Server administration / Server Maintenance: Cleanup, Backup, and Restoration ✍️ 🧐
• Galaxy Server administration / Galaxy Interactive Tools 🧐
• Galaxy Server administration / Distributed Object Storage 🧐
• Galaxy Server administration / External Authentication 🧐
• Galaxy Server administration / Performant Uploads with TUS ✍️ 🧐
• Galaxy Server administration / Galaxy Tool Management with Ephemeris 🧐
• Galaxy Server administration / Ansible 🧐
• Galaxy Server administration / Mapping Jobs to Destinations using TPV 🧐
• Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
• Galaxy Server administration / Use Apptainer containers for running Galaxy jobs 🧐
• Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses 🧐
• Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP 🧐

Slides

• Epigenetics / Introduction to ATAC-Seq data analysis ✍️
• Epigenetics / Introduction to DNA Methylation data analysis 🧐
• Transcriptomics / Identification of non-canonical ORFs and their potential biological function 📝 🧐
• Galaxy Server administration / Galaxy Installation with Ansible 🧐
• Galaxy Server administration / Galaxy Administrator Time Burden and Technology Usage 🖥
• Galaxy Server administration / Controlling Galaxy with systemd or Supervisor 🧐
• Galaxy Server administration / Server Maintenance: Cleanup, Backup, and Restoration 🧐

FAQs

• Automatically trim adapters (without providing custom sequences)
• In bowtie 2 parameters, in place of 1000 for other experiments, should we mention the median fragment length observed in our library?
• Creating a paired collection
• Changing the datatype
• Converting the file format
• Updating from 22.01 to 23.0 with Ansible
• Changing the heatmap colours
• Copy a dataset between histories
• Is it possible to subsample some samples if you have more reads?
• UCSC import: what should my file look like?

Video Recordings

• Epigenetics / Introduction to ATAC-Seq data analysis 💬 🗣
• Transcriptomics / Reference-based RNA-Seq data analysis 💬 🗣

Events

• Galaxy Training Academy 2024 🧑‍🏫

GitHub Activity

github Issues Reported

38 Merged Pull Requests

See all of the github Pull Requests and github Commits by Lucille Delisle.

• CUT&RUN: Fix zenodo link (left from ATAC copy paste)
  epigenetics
• Update CUT&RUN tutorial
  epigenetics
• update training for CYOA if space in option
  contributing
• Fix CYOA of collection split in Ref-based
  transcriptomics
• Add a third way to run DESeq2 in Ref-based tuto
  transcriptomics

Reviewed 29 PRs

We love our community reviewing each other's work!

• Update CONTRIBUTORS.yaml
  template-and-tools
• Update CUT and RUN tutorial
  epigenetics
• Update CUT&RUN tutorial
  epigenetics
• Add a third way to run DESeq2 in Ref-based tuto
  transcriptomics
• Update FAQ about 22.01 to 23.0
  admin

News

External Links

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