New Tutorial: Downstream Single-cell RNA Plant analysis with ScanPy

new tutorial single-cell plant

Posted on: 30 March 2021 purlPURL: https://gxy.io/GTN:N00009

Single cell RNA-seq analysis is a cornerstone of developmental research and provides a great level of detail in understanding the underlying dynamic processes within tissues. In the context of plants, this highlights some of the key differentiation pathways that root cells undergo.

This tutorial replicates the paper Denyer et al. 2019, where the major plant cell types are recovered in the data as well as distinguishing between QC and meristematic cells.

View Material

References

  1. Denyer, T., X. Ma, S. Klesen, E. Scacchi, K. Nieselt et al., 2019 Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing. Developmental Cell 48: 840–852.e5. 10.1016/j.devcel.2019.02.022

Recent News

See all news

Scaling Up Hands-On Bioinformatics Training with TIAAS – An Open University Perspective

3 July 2025   gtn TIAAS

Back in September 2024, we ran the Open University Bioinformatics Bootcamp—a free, five-day online course introducing students to the core tools and techniques used in single-cell biology. We were genuinely delighted by the level of interest: 120 students signed up, 100 showed up, and around 80 worked through the hands-on tutorials during the week. That’s a fantastic level of engagement, especially for a course that’s entirely optional and doesn’t count towards their degree.

Enhancing Scientific Training: The Galaxy Training Network's Role in the ELIXIR Training Life-Cycle

1 July 2025   gtn

In the rapidly evolving landscape of data science, continuous learning and skill development are crucial. The Galaxy Training Network (GTN) plays a pivotal role in this educational ecosystem, particularly within the ELIXIR Training Life-Cycle. This blog post explores how the GTN contributes to each phase of the life-cycle and aligns with the SPLASH recommendations, ensuring high-quality training for researchers worldwide.

An Ode to the Galaxy Community and all I learned

19 June 2025   gtn

This is my ode to the Galaxy Community to say how grateful I have been for your welcome, your energy, and your support. I have learned so very, very much, about bioinformatics; about software development; and most of all, about open-source communities in this complex scientific world.