¡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 StoryWendi 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.
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.
- 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
- 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
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 🧑🏫
News
Author(s) | Wendi Bacon Mehmet 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 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 StoryAuthor(s) | 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 StoryAuthor(s) | Helena Rasche |
Tester(s) | Wendi Bacon |
We at the GTN strive to bring you the most fun and fancy features we can in a completely static site! Today we’re addressing the question of Wendi Bacon who needed a solution for keeping her single cell subdomain up-to-date with all the latest happenings in the Single Cell world.
Full StoryAuthor(s) | Wendi Bacon Pavankumar Videm |
Infrastructure | José Manuel Domínguez |
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 StoryAuthor(s) | Mehmet Tekman Wendi Bacon Pavankumar Videm |
🚀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 StoryAuthor(s) | Julia Jakiela Morgan Howells Wendi Bacon |
New single cell section: Changing data formats & preparing objects
Full StoryAuthor(s) | Helena Rasche |
Tester(s) | Wendi Bacon |
Infrastructure | Helena Rasche |
Based on user feedback of the difficulties of the GTN news submission process we have significantly simplified and removed the need for manually editing a YAML file by providing a quick and easy Google Form
Full StoryAuthor(s) | Helena Rasche Jennifer Hillman-Jackson Wendi Bacon Martin Čech |
Tester(s) | Jennifer Hillman-Jackson |
Infrastructure | Helena Rasche |
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 StoryAuthor(s) | Camila Goclowski |
Editor(s) | Wendi Bacon |
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.
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