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.

1 Editorial Role

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

53 Tutorials

• Proteomics / metaQuantome 1: Data creation 🧐
• Introduction to Galaxy Analyses / How to reproduce published Galaxy analyses 🧐
• Single Cell / Understanding Barcodes 🧐
• Galaxy Server Administration / Galaxy Monitoring with gxadmin 🧐
• Galaxy Server Administration / Galaxy Installation with Ansible 📝 🧐
• Galaxy Server Administration / Ansible 🧐
• Galaxy Server Administration / Galaxy Monitoring with Telegraf and Grafana 🧐
• Galaxy Server Administration / Reference Data with CVMFS without Ansible 🧐
• Galaxy Server Administration / Data Libraries 🧐
• Galaxy Server Administration / Setting up Celery Workers for Galaxy 🧐
• Galaxy Server Administration / Mapping Jobs to Destinations using TPV 🧐
• Galaxy Server Administration / Deploying Wireguard for private mesh networking 🧐
• Galaxy Server Administration / Running Jobs on Remote Resources with Pulsar 🧐
• Galaxy Server Administration / Galaxy Monitoring with Reports 🧐
• Galaxy Server Administration / Galaxy Interactive Tools 🧐
• Galaxy Server Administration / External Authentication 🧐
• Galaxy Server Administration / Use Apptainer containers for running Galaxy jobs 📝 🧐
• Galaxy Server Administration / Reference Data with CVMFS 🧐
• Galaxy Server Administration / Galaxy Tool Management with Ephemeris 🧐
• Galaxy Server Administration / Automation with Jenkins 🧐
• Galaxy Server Administration / Connecting Galaxy to a compute cluster 🧐
• Galaxy Server Administration / Training Infrastructure as a Service (TIaaS) 🧐
• Galaxy Server Administration / Performant Uploads with TUS ✍️ 🧐
• Galaxy Server Administration / Distributed Object Storage 🧐
• Galaxy Server Administration / Enable upload via FTP ✍️ 🧐
• Galaxy Server Administration / Server Maintenance: Cleanup, Backup, and Restoration ✍️ 🧐
• Variant Analysis / Trio Analysis using Synthetic Datasets from RD-Connect GPAP 🧐
• Contributing to the Galaxy Training Material / Creating a new tutorial ✍️
• Contributing to the Galaxy Training Material / Updating diffs in admin training 🧐
• Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
• 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 🧐
• Transcriptomics / Visualization of RNA-Seq results with heatmap2 📝
• Transcriptomics / Genome-wide alternative splicing analysis ✍️ 🧐
• Using Galaxy and Managing your Data / Group tags for complex experimental designs 🧐
• Using Galaxy and Managing your Data / Understanding Galaxy history system 🧐
• Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters 🧐
• Epigenetics / ATAC-Seq data analysis ✍️ 🧐
• Epigenetics / CUT&RUN data analysis 📝 🧐
• Transcriptomics / Referenzbasierte RNA-Seq-Datenanalyse ✍️
• Transcriptomics / Análisis de datos RNA-Seq basados en referencias ✍️
• Transcriptomics / Analisi dei dati RNA-Seq basata su riferimenti ✍️

8 Slides

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

19 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?
• Creación de una colección emparejada ✍️
• Creating a paired collection
• Erstellen einer gepaarten Sammlung ✍️
• Creazione di una raccolta accoppiata ✍️
• Publish your workflow in IWC
• Changing the datatype
• Ändern des Datentyps ✍️
• Modifica del tipo di dato ✍️
• Converting the file format
• Updating from 22.01 to 23.0 with Ansible
• Changing the heatmap colours
• Copiar un conjunto de datos entre historiales ✍️
• Copy a dataset between histories
• Kopieren eines Datensatzes zwischen Historien ✍️
• Copiare un set di dati tra le cronologie ✍️
• Is it possible to subsample some samples if you have more reads?
• UCSC import: what should my file look like?

10 Video Recordings

• Epigenetics / Introduction to ATAC-Seq data analysis 💬 🗣
• Transcriptomics / Reference-based RNA-Seq data analysis 💬 🗣
• Transcriptomics / Referenzbasierte RNA-Seq-Datenanalyse 💬 🗣
• Transcriptomics / Análisis de datos RNA-Seq basados en referencias 💬 🗣
• Transcriptomics / Analisi dei dati RNA-Seq basata su riferimenti 💬 🗣

1 Event

• Galaxy Training Academy 2024 🧑‍🏫

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GitHub Activity

github Issues Reported

46 Merged Pull Requests

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

• Add a FAQ to guide users to IWC guidelines
  faqs
• change tool name in FAQ concatenate
  faqs
• Small ref based changes
  transcriptomics
• Update rna-seq-viz tutorial
  transcriptomics
• Update ref based tools
  transcriptomics

Reviewed 34 PRs

We love our community reviewing each other's work!

• Update CUT&RUN tutorial with deeptools 4
  epigenetics
• Update the ATAC-seq tutorial with deepTools4
  epigenetics
• [GAT] Fix slurm and tpv trainings
  admin
• add the SSA link to the Admin topic
  admin
  template-and-tools
  single-cell
• updating Reference-based RNA-Seq data analysis
  transcriptomics

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