¡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.
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
- Using Galaxy and Managing your Data / JupyterLab in Galaxy 🧐
- Single Cell / Importing files from public atlases ✍️ 🧐
- Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat 🧐
- Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat (R) 📝 🧐
- Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy ✍️ 🧐
- Single Cell / Combining single cell datasets after pre-processing ✍️ 🧐
- Single Cell / Removing the effects of the cell cycle 📝 🧐
- Single Cell / Analysis of plant scRNA-Seq Data with Scanpy 🧐
- Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets 🧐
- Single Cell / Scanpy Parameter Iterator ⚙️
- Single Cell / Inferring single cell trajectories with Monocle3 📝 ⚙️ 🧐
- Single Cell / Inferring single cell trajectories with Scanpy (Python) ✍️ 🧐
- Single Cell / Converting NCBI Data to the AnnData Format 📝 🧐
- Single Cell / Generating a single cell matrix using Alevin ✍️ 🧐
- Single Cell / Converting between common single cell data formats ✍️
- Single Cell / Bulk RNA Deconvolution with MuSiC ✍️ 🧐
- Single Cell / Generating a single cell matrix using Alevin and combining datasets (bash + R) ✍️ 🧐
- Single Cell / Comparing inferred cell compositions using MuSiC deconvolution ✍️ 🧐
- Single Cell / Inferring single cell trajectories with Scanpy ✍️ 🧐
- Single Cell / Clustering 3K PBMCs with Scanpy 🧐
- Single Cell / Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution ✍️ 🧐
- Single Cell / Pre-processing of 10X Single-Cell RNA Datasets ✍️ 🧐
- Single Cell / Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution ✍️ 🧐
- Single Cell / Inferring single cell trajectories with Monocle3 (R) 📝 🧐
- Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) ✍️ 🧐
- Single Cell / Understanding Barcodes 🧐
- Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data 📝
- Ecology / Sentinel 2 biodiversity 🧐
- FAIR Data, Workflows, and Research / FAIR Galaxy Training Material 🧐
- Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
- Contributing to the Galaxy Training Material / Principles of learning and how they apply to training and teaching 🧐
- Contributing to the Galaxy Training Material / Updating tool versions in a tutorial ✍️ 🧐
- Foundations of Data Science / Python - Type annotations 🧐
- Foundations of Data Science / Python - Lists & Strings & Dictionaries 🧐
- Foundations of Data Science / Python - Testing 🧐
- Foundations of Data Science / Python - Multiprocessing 🧐
- Foundations of Data Science / Python - Try & Except 🧐
- Foundations of Data Science / Python - Functions 🧐
- Foundations of Data Science / Python - Files & CSV 🧐
- Foundations of Data Science / Python - Globbing 🧐
- Foundations of Data Science / Python - Math 🧐
- Foundations of Data Science / Python - Loops 🧐
- Foundations of Data Science / Python - Flow Control 🧐
- Foundations of Data Science / Python - Basic Types & Type Conversion 🧐
- Foundations of Data Science / Python - Subprocess 🧐
- Foundations of Data Science / Python - Introductory Graduation 🧐
- Development in Galaxy / Adding and updating best practice metadata for Galaxy tools using the bio.tools registry 📝
- Introduction to Galaxy Analyses / A short introduction to Galaxy 🧐
- Galaxy Community Building / Creation of an interactive Galaxy tools table for your community 🧐
- Galaxy Community Building / What's a Special Interest Group? ✍️ 🧐
- Galaxy Community Building / Creating a Special Interest Group ✍️ 🧐
- 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 ✍️ 🧐
- Single Cell / Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin ✍️ 🧐
- Introduction to Galaxy Analyses / Breve introducción a Galaxy - en español 🧐
Slides
- Single Cell / Trajectory analysis 🧐
- Single Cell / Plates, Batches, and Barcodes ✍️ 🧐
- Single Cell / An introduction to scRNA-seq data analysis 🧐
- Single Cell / Automated Cell Annotation 🧐
- Single Cell / Single-cell Formats and Resources ✍️
- Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data ✍️
- Introduction to Galaxy Analyses / A Short Introduction to Galaxy 🧐
- Single Cell / Introducción al análisis de datos de scRNA-seq ✍️ 🧐
- Introduction to Galaxy Analyses / Una breve introducción a Galaxy ✍️
- Single Cell / Una introducción al análisis de datos scRNA-seq 🧐
- Introduction to Galaxy Analyses / Una Breve Introducción a Galaxy 🧐
FAQs
- Add Toolshed category to a tool
- Why is Alevin is not working?
- Why is Alevin is not working?
- Why is amplification more of an issue in scRNA-seq than RNA-seq?
- AnnData Import/ AnnData Manipulate not working?
- How do I add my community to the Galaxy CoDex?
- Cambiar el tipo de datos
- Importing via links
- Importación por medio de enlaces
- Uso del cuaderno de apuntes para ver varios conjuntos de datos
- My Scanpy FindMarkers step is giving me an empty table
- What's the Galaxy Community Board?
- How do I join the Galaxy Community Board?
- What is the Galaxy Governance Structure?
- Using tutorial mode and the Case Study suite
- Using Answer Key Histories
- Créer un nouvel history
- Creating a new history
- Para la creación de un historial nuevo
- Cambiando el nombre de un historial
- Compartiendo un historial
- Input Histories & Answer Keys
- Launch JupyterLab
- How can I plan meetings across timezones?
- Notebook-based tutorials can give different outputs
- On Scanpy PlotEmbed, the tool is failing
- On the Scanpy PlotEmbed step, my object doesn’t have Il2ra or Cd8b1 or Cd8a etc.
- How do I know what protocol my data was sequenced with?
- Are Barcodes always on R1 and Sequence data on R2?
- Request Galaxy tools on a specific server
-
Why is my tool erroring as 'Above error raised while reading key '/layers' of type
from /.' - Use our Single Cell Omics Lab
- Can RNA-seq techniques be applied to scRNA-seq?
- Para volver a ejecutar una herramienta
- Using tutorial mode
- The UMAP Plots errors out sometimes?
- Are UMIs not actually unique?
- How can I talk with other users?
- Using answer key histories
- Extraer un flujo de trabajo de tu historial
Video Recordings
- Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy 💬 🗣
- Single Cell / Combining single cell datasets after pre-processing 💬 🗣
- Single Cell / Inferring single cell trajectories with Scanpy (Python) 💬 🗣
- Single Cell / Generating a single cell matrix using Alevin 💬 🗣
- Single Cell / Bulk RNA Deconvolution with MuSiC 💬 🗣
- Single Cell / Clustering 3K PBMCs with Scanpy 🗣
- Single Cell / Pre-processing of 10X Single-Cell RNA Datasets 🗣
- Single Cell / Understanding Barcodes 🗣
Events
- 2024 Bioinformatics Bootcamp - The Open University 🎪 🧑🏫
- Single-cell and sPatial Omics | Collaboration Fest 🎪
- Galaxy Training Academy 2024 🧑🏫
GitHub Activity
github Issues Reported
116 Merged Pull Requests
See all of the github Pull Requests and github Commits by Wendi Bacon.
-
SPOC CoFest blog post
news
-
Welcome new SPOC Editorial Board members!
single-cell
-
Update CoDex tutorial and make an FAQ
template-and-tools
-
Update single-cell topic layout and content
template-and-toolssingle-cell
-
Update request-galaxy-tools-on-a-specific-server.md
faqs
Reviewed 87 PRs
We love our community reviewing each other's work!
-
SPOC CoFest blog post
news
-
Update slides.html
single-cellspoc-cofest
-
Add adya29 as contributor
template-and-toolsspoc-cofest
-
Add GokceOGUZ as contributor
template-and-toolsspoc-cofest
-
Add adairama as contributor
template-and-toolsspoc-cofest
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 Tekman and 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.
Full StoryAuthor(s) | Helena Rasche Wendi Bacon |
Infrastructure | Helena Rasche |
We would like to recognise and thank all of the reviewers who have contributed to the GTN tutorials; your efforts are greatly appreciated, and we are grateful for your contributions to the GTN community. Today, we are highlighting your efforts on every single learning material across the GTN.
Full StoryExternal Links
Favourite Topics
Favourite Formats