Lecturer at The Open University
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
Tutorials
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Single Cell
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Inferring Trajectories using Scanpy - Jupyter Notebook
✍️
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Single Cell
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Trajectory Analysis using Monocle3
📝
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Single Cell
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Trajectory Analysis using Monocle3
⚙️
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Single Cell
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Comparing inferred cell compositions using MuSiC deconvolution
✍️
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Single Cell
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Removing the effects of the cell cycle
📝
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Single Cell
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Pre-processing of 10X Single-Cell RNA Datasets
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Single Cell
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Filter, Plot and Explore Single-cell RNA-seq Data
✍️
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Single Cell
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Creating the bulk RNA-seq dataset for deconvolution
✍️
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Single Cell
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Bulk RNA Deconvolution with MuSiC
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Single Cell
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Creating the single-cell RNA-seq reference dataset for deconvolution
✍️
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Single Cell
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Generating a single cell matrix using Alevin
✍️
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Single Cell
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Combining datasets after pre-processing
✍️
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Single Cell
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Filtrado, representación y exploración de secuenciación de ARN de células únicas
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Single Cell
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Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin
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Single Cell
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Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin
Slides
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Single Cell
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Plates, Batches, and Barcodes
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Single Cell
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Introducción al análisis de datos de scRNA-seq
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Introduction to Galaxy Analyses
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Una breve introducción a Galaxy
News
29 November 2022
Authors: 
Mehmet Tekman
Wendi Bacon
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
18 November 2022
Authors: Wendi BaconMehmet Tekman
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!
Full Story
20 May 2021
¡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.
Full Story
Mehmet TekmanWendi Bacon
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
Wendi BaconMehmet Tekman
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!
Full Story
Beatriz Serrano-Solano
Patricia Carvajal López
Alejandra Escobar-Zepeda
Saskia Hiltemann
Helena Rasche¡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.
Full Story