Feb 07, 2024
Gene set enrichment analysis
- 1University of Oxford
Protocol Citation: Peter Kilfeather 2024. Gene set enrichment analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.kxygx3d2wg8j/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 07, 2024
Last Modified: February 07, 2024
Protocol Integer ID: 94808
Funders Acknowledgement:
Aligning Science Across Parkinson's
Grant ID: ASAP-020370
Monument Trust Discovery Award from Parkinson’s UK
Grant ID: J-1403
Abstract
Gene set enrichment analysis from Kilfeather, Khoo et al., 2024
Protocol
Protocol
No statistical methods were used to predetermine sample sizes, but our sample sizes for TRAP analyses surpass those reported in previous publications23,28,87 and our sample sizes for Stereo-seq samples are comparable with or exceed those of similar spatial transcriptomic datasets11. All statistical analyses were performed with R (v4.2.1) and Python (v3.9). All P values were modified to an FDR of 1, 5 or 10 % as described in the text with the Benjamini & Hochberg method.