Warning: Please be aware that these videos are a snapshot, and as such may use an outdated version of the tutorial and/or Galaxy. Below the video you will find links to the tutorials as they appeared at the time of recording.
Analysis of plant scRNA-Seq Data with Scanpy
Below are video tutorials for this GTN material, created for various (past) events.
Tutorial Video (February 2021)
This tutorial replicates the paper “Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing” (Denyer et al. 2019), where the major plant cell types are recovered in the data as well as distinguishing between QC and meristematic cells. The original paper used the Seurat analysis suite (Satija et al. 2015), but here we will use the ScanPy analysis suite (Wolf et al. 2018) integrated within the single-cell resources in Galaxy (Tekman et al. 2020).