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Lecturer at The Open University

nomadscientist
wendi.bacon@open.ac.uk
nomadscientist:matrix.org
WendiBacon1
0000-0002-8170-8806
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Favourite Topics

Favourite Formats

Wendi Bacon

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

New Tutorial Suite: Deconvolution with MuSiC, from public data to disease interrogation!
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.

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New Topic: Single Cell Analysis!
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 byWendi 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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¿Hablas español?: The first curated tutorial in Spanish!
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 Patricia Carvajal López y Alejandra Escobar-Zepeda (EMBL-EBI) así 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 traducción y mantenimiento y, por supuesto, a Wendi Bacon (The Open University/EBI) como líder de proyecto.

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