Wendi Bacon

Lecturer at The Open University

Contributions

The following list includes only slides and tutorials where the individual 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.

GitHub Activity

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.

Tutorials

Slides

News

screenshot of the Single Cell Omics subdomain page, with purple mastheader, Single Cell Tools categories along the side, and an updated logo combining the Single Cell Omics connected cells image with the Human Cell Atlas blue embyro logo
12 October 2023
gtn singlecell

The European Galaxy Days 2023 CoFest combined the forces of administrator, developer and trainer to update and re-launch the single cell Galaxy instance. Where previously there were two subdomains each with their own sets of tools, there is now a unified subdomain with re-categorized tools that makes sense for users.

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Heatmap with columns of cell types vs rows of inferred and actual cell type proportions for A and B samples. Cell colours are similar between actual and inferred.
29 November 2022
new tutorial single-cell transcriptomics

The still new and shiny single-cell analysis topic now boasts a deconvolution tutorial suite! What does deconvolution do you ask? Well, in this context, it infers cell proportions from bulk RNA-seq data. You heard that correctly - instead of expensive new single-cell experiments, you can re-analyse old bulk RNA-seq data and estimate cell proportions. All you need is a reasonably good single cell dataset to use as a reference and you鈥檙e good to go! The tutorial suite shows you how to build your reference from publicly available single cell data, and apply analysis to some publicly available bulk RNA-seq data.

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Pretty dots of different colours combined into two cell cluster plots on the sides. In the middle, a split violin plot showing the expression of unknown genes in blue on one side and the expression of the genes in an opposing sample in orange alongside. Snuck in between these three important plots is a PhD comic of data showing no trend, with the chat box 鈥淗mm鈥 I think there鈥檚 a clear trend happening here.鈥
18 November 2022
new topic single-cell new feature

Single-cell analysis now has it鈥檚 own topic! These tutorials were previously part of the transcriptomics topic, but due to the amazing efforts by Wendi Bacon, Mehmet Tekmanand others, we now have so many single-cell analysis tutorials that they deserve their own dedicated topic! From introductory slides and practicals, to case study tutorials generating cell clusters and trajectories from raw sequencing files, and even a growing subtopic of smaller tips and tricks for adapting analysis to user needs, the single cell topic either has what you need or is working on it. Come learn or get involved!

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Hello in many languages
20 May 2021
new tutorial espa帽ol

隆El primer tutorial en espa帽ol ya est谩 disponible! Galaxy siempre ha tenido tutoriales traducidos autom谩ticamente mediante Google-Translate, ahora nos estamos embarcando en un nuevo proyecto para estudiar la experiencia de aprendizaje con tutoriales en bioinform谩tica traducidos por humanos. Nuestro objetivo es crear un paquete de tutoriales para el an谩lisis de datos single-cell (c茅lula 煤nica) en primera instancia, con el fin de estudiar su uso y utilidad en un taller para hablantes nativos de espa帽ol. Agradecemos enormemente a las nuevas participantes Patricia Carvajal L贸pez y Alejandra Escobar-Zepeda (EMBL-EBI) as铆 como a las miembros existentes de GTN Beatriz Serrano-Solano (University of Freiburg), Saskia Hiltemann & Helena Rasche (Erasmus-MC), por su arduo trabajo en este proyecto de traducci贸n y mantenimiento y, por supuesto, a Wendi Bacon (The Open University/EBI) como l铆der de proyecto.

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