Wendi Bacon

Lecturer at The Open University

Affiliations

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

Video Recordings

News

Hello in many languages
20 May 2021
new tutorial español

¡El primer tutorial en español ya está disponible! Galaxy siempre ha tenido tutoriales traducidos automáticamente mediante Google-Translate, ahora nos estamos embarcando en un nuevo proyecto para estudiar la experiencia de aprendizaje con tutoriales en bioinformática traducidos por humanos. Nuestro objetivo es crear un paquete de tutoriales para el análisis de datos single-cell (célula única) en primera instancia, con el fin de estudiar su uso y utilidad en un taller para hablantes nativos de español. Agradecemos enormemente a las nuevas participantes @gtn:pclo y @gtn:ales-ibt (EMBL-EBI) así como a las miembros existentes de GTN @gtn:beatrizserrano (University of Freiburg), @gtn:shiltemann & @gtn:hexylena (Erasmus-MC), por su arduo trabajo en este proyecto de traducción y mantenimiento y, por supuesto, a @gtn:nomadscientist (The Open University/EBI) como líder de proyecto.

Full Story
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 “Hmm… I think there’s a clear trend happening here.”
18 November 2022
new topic single-cell new feature

Single-cell analysis now has it’s 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!

Full Story
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’re 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.

Full Story
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.

Full Story
swirled cluster dots surround a circle of people all holding hands, looking towards the bright center (future)
22 December 2023
gtn communications single-cell

🚀Embarking on a cosmic journey, the Galaxy Single-cell Community has clustered together to unveil a constellation of tools, making strides in RNA-stellar discoveries and creating out-of-this-world workflows. With a commitment to battling work duplication across the multiverse, this community is boldly charting a course for global domination, proving that when it comes to bioinformatics, the Galaxy is the limit!✨

Full Story
GTN logo with a multi-coloured star and the words Galaxy Training Network
30 January 2024
gtn infrastructure new feature beta

Howdy teachers and support staff! We are exploring displaying GTN content directly in the Galaxy Help site, furthering the integration between the GTN and the Galaxy community infrastructure. When you paste a GTN Frequently Asked Questions URL into the Galaxy Discourse, it will now be rendered directly in Discourse!

Full Story
GTN logo with a multi-coloured star and the words Galaxy Training Network
13 June 2024
Author(s) Camila Goclowski avatar Camila Goclowski
Editor(s) orcid logoWendi Bacon avatar Wendi Bacon
single-cell training education trajectory user contributor

With growing access and interest in sequencing data, Galaxy is a knight in shining armor for wet lab scientists hoping to analyze their own data. With long term intentions of increasing access to bioinformatic analyses, the Galaxy Training Network (GTN) creates a safe space where non-computer-scientists may analyze their own data and even learn to code: an invaluable skill in today’s scientific world. Galaxy introduced me to brand new skills as an undergraduate and ultimately changed the trajectory of my career. Here is my story as a biology undergraduate with no coding experience turned GTN contributor &, eventually, coding bioinformatician: thanks to Galaxy.

Full Story