CytoTools is a toolbox of scripts that are useful for cytometry data management. Many of these are designed to be used in conjunction with the 'Cytometry Analysis Pipeline for large and compleX data' (CAPX) discovery analysis approach (https://github.com/sydneycytometry/CAPX).
SumTables is script that generates summary data after clustering (such as number of cells per cluster per sample, MFI of various markers per cluster etc).
HeatMaps is a flexible script intended to create phenotype heatmaps (i.e. MFI of selected markers vs clusters), difference heatmaps (number of cells or MFI per cluster vs samples) and fold-change heatmaps.
SampleMerge facilitates the merging of multiple separate samples (as .csv files) into one large file.
SampleSplit facilitates the splitting of multiple separate samples out of one large file .csv file.
Associated scripts
AutoGraph (https://github.com/sydneycytometry/AutoGraph) can be used to automatically plot dot plots to compare measurements (cells per tissue, median fluorescence intensity (MFI) etc) of each cluster/population between groups.
tSNEplots (https://github.com/sydneycytometry/tSNEplots) can be used to automatically create coloured tSNE plots.
Download CytoTools scripts
Go to 'releases' above (https://github.com/sydneycytometry/CytoTools/releases) and download source code for the latest version of the CytoTools scripts.
Protocols
For usage instructions, please see https://github.com/sydneycytometry/CytoTools/wiki
If you use these scripts in your work, please cite this github using the information below. You can cite the specific version that you used in your work.
Ashhurst, T. M. (2019). CytoTools v1.0. GitHub repository. Repository: https://github.com/sydneycytometry/CytoTools
Packages used
TBC