This template markdown aims to facilitate and automate the analysis of tabular output data generated by CiliaQ. It searches, fetches and joins all CiliaQ output files ('_CQs.txt') allowing downstream analysis in R or to export the collected data as an .xslx (Excel) file. Additionally, the script implements basic quality control steps and aims to create a brief overview of the retrieved data.
Downlaod the repository or directly clone the project using Git. The script was written and tested in R version 4.0.0, however, earlier versions might be functional, as well.
Note: You should clone the whole project structure, as it also contains the blueprints of additional documents (exclude lists, annotation lists) and custom functions imported into the actual script.
Before running the script only the paths, names, and experimental conditions need to be modified (marked with the tag 'TODO'). Hence, running the script does not require (higher) skills in R programming. All the steps are explained in the markdown parts of the documents.
Hansen JN, Rassmann S, Stüven B, Jurisch-Yaksi N, Wachten D. CiliaQ: a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images. Eur Phys J E Soft Matter. 2021 Mar 8;44(2):18. doi: 10.1140/epje/s10189-021-00031-y. PMID: 33683488.