Plant lovers are in luck! A new tutorial on this fascinating kingdom has been added to the GTN. It details the necessary steps to identify potential targets of brassinosteroid-induced miRNAs. Brassinosteroids are phytohormones that have the ability to stimulate plant growth and confer resistance against abiotic and biotic stresses. These characteristics have led to great interest in the field of biotechnology due to its potential for increasing agricultural productivity.
Full StoryPavankumar Videm
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.
- Single Cell
- Applying single-cell RNA-seq analysis
- Introduction to Galaxy and Single Cell RNA Sequence analysis
Tutorials
- Single Cell / Converting between common single cell data formats ⚙️
- Single Cell / Generating a single cell matrix using Alevin and combining datasets (bash + R) 📝 ⚙️
- Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat (R) 📝
- Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets
- Single Cell / Analysis of plant scRNA-Seq Data with Scanpy
- Single Cell / Inferring single cell trajectories with Scanpy 📝
- Single Cell / Clustering 3K PBMCs with Scanpy
- Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 📝 ⚙️
- Single Cell / Pre-processing of 10X Single-Cell RNA Datasets
- Single Cell / Filter, plot, and explore single cell RNA-seq data with Seurat 📝
- Single Cell / Converting NCBI Data to the AnnData Format 📝 ⚙️
- Single Cell / Inferring single cell trajectories with Monocle3 (R) 📝
- Transcriptomics / Reference-based RNA-Seq data analysis ✍️
- Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana
- Transcriptomics / Small Non-coding RNA Clustering using BlockClust
- Transcriptomics / RNA-RNA interactome data analysis
- Transcriptomics / Genome-wide alternative splicing analysis 📝
- Epigenetics / Formation of the Super-Structures on the Inactive X
Slides
Video Recordings
Events
News
Author(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 Story