Wendi Bacon

Senior Lecturer at The Open University

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.

• Galaxy Community Building
• Single Cell
• Applying single-cell RNA-seq analysis
• Building training material in Galaxy
• Introduction to Galaxy and Single Cell RNA Sequence analysis
• Applying single-cell RNA-seq analysis in Coding Environments

Tutorials

• Development in Galaxy / Adding and updating best practice metadata for Galaxy tools using the bio.tools registry 📝
• Single Cell / Scanpy Parameter Iterator ⚙️
• Single Cell / Generating a single cell matrix using Alevin ✍️
• Single Cell / Inferring single cell trajectories with Monocle3 (R) 📝
• Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data 📝
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) ✍️
• Single Cell / Removing the effects of the cell cycle 📝
• Single Cell / Converting NCBI Data to the AnnData Format 📝
• Single Cell / Converting between common single cell data formats ✍️
• Single Cell / Pre-processing of 10X Single-Cell RNA Datasets
• Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat (R) 📝
• Single Cell / Inferring single cell trajectories with Scanpy (Python) ✍️
• Single Cell / Generating a single cell matrix using Alevin and combining datasets (bash + R) ✍️
• Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution ✍️
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy ✍️
• Single Cell / Inferring single cell trajectories with Scanpy ✍️
• Single Cell / Bulk RNA Deconvolution with MuSiC
• Single Cell / Comparing inferred cell compositions using MuSiC deconvolution ✍️
• Single Cell / Combining single cell datasets after pre-processing ✍️
• Single Cell / Importing files from public atlases ✍️
• Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution ✍️
• Single Cell / Inferring single cell trajectories with Monocle3 📝 ⚙️
• Galaxy Community Building / What's a Special Interest Group? ✍️
• Galaxy Community Building / Creating a Special Interest Group ✍️
• Single Cell / Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin
• Single Cell / Filtrado, representación y exploración de secuenciación de ARN de células únicas
• Single Cell / Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin

Slides

• Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data
• Single Cell / Single-cell Formats and Resources
• Single Cell / Plates, Batches, and Barcodes
• Single Cell / Introducción al análisis de datos de scRNA-seq
• Introduction to Galaxy Analyses / Una breve introducción a Galaxy

FAQs

• Add Toolshed category to a tool
• Why is Alevin is not working?
• Why is Alevin is not working?
• Why is amplification more of an issue in scRNA-seq than RNA-seq?
• AnnData Import/ AnnData Manipulate not working?
• Cambiar el tipo de datos
• Importing via links
• Importación por medio de enlaces
• Uso del cuaderno de apuntes para ver varios conjuntos de datos
• My Scanpy FindMarkers step is giving me an empty table
• What's the Galaxy Community Board?
• How do I join the Galaxy Community Board?
• What is the Galaxy Governance Structure?
• Using tutorial mode and the Case Study suite
• Using Answer Key Histories
• Creating a new history
• Para la creación de un historial nuevo
• Créer un nouvel history
• Cambiando el nombre de un historial
• Compartiendo un historial
• Input Histories & Answer Keys
• Launch JupyterLab
• How can I plan meetings across timezones?
• Notebook-based tutorials can give different outputs
• On Scanpy PlotEmbed, the tool is failing
• On the Scanpy PlotEmbed step, my object doesn’t have Il2ra or Cd8b1 or Cd8a etc.
• How do I know what protocol my data was sequenced with?
• Are Barcodes always on R1 and Sequence data on R2?
• Request Galaxy tools on a specific server
• Why is my tool erroring as 'Above error raised while reading key '/layers' of type from /.'
• Use our Single Cell Omics Lab
• Can RNA-seq techniques be applied to scRNA-seq?
• Para volver a ejecutar una herramienta
• Using tutorial mode
• The UMAP Plots errors out sometimes?
• Are UMIs not actually unique?
• How can I talk with other users?
• Using answer key histories
• Extraer un flujo de trabajo de tu historial

Video Recordings

• Single Cell / Generating a single cell matrix using Alevin 💬 🗣
• Single Cell / Clustering 3K PBMCs with Scanpy 🗣
• Single Cell / Pre-processing of 10X Single-Cell RNA Datasets 🗣
• Single Cell / Understanding Barcodes 🗣
• Single Cell / Inferring single cell trajectories with Scanpy (Python) 💬 🗣
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy 💬 🗣
• Single Cell / Bulk RNA Deconvolution with MuSiC 💬 🗣
• Single Cell / Combining single cell datasets after pre-processing 💬 🗣

Events

• 2024 Bioinformatics Bootcamp - The Open University 🎪 🧑‍🏫
• Single-cell and sPatial Omics | Collaboration Fest 🎪
• Galaxy Training Academy 2024 🧑‍🏫

GitHub Activity

github Issues Reported

108 Merged Pull Requests

See all of the github Pull Requests and github Commits by Wendi Bacon.

• add registration link to SPOC CoFest
  template-and-tools
• Update biotools
  dev
• update learning pathways for seurat and scanpy
  template-and-tools
• Fix FAQ format
  single-cell
• Added MIGHTS tag
  single-cell

Reviewed 80 PRs

We love our community reviewing each other's work!

• [Community Tool Table Generation] Update the process to curate TS filtered community tool table
  dev
• Implement compat matrix on maintainer page
  template-and-tools
  contributing
• match updated Scanpy fa2-modified, add an option to download input data
  single-cell
• fix default
  single-cell
• Updating input history link in text
  single-cell

News

External Links

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