HDStIM package is published on CRAN at https://cran.r-project.org/package=HDStIM. The documentation website is https://niaid.github.io/HDStIM/. Preprint with the conceptual framework https://www.biorxiv.org/content/10.1101/2022.11.14.516371v1.

1. Running all the functions of HDStIM using the builtin package data

scr00_00_run_hdstim_with_package_data.R

These are a set of helper scripts to set up and execute HDStIM on the cell population - stimulation combinations derived from manually gated FCS files.

2. Concatenate per population FSC files into a data frame Note: this step is not required if the data is exported from the Robinson's pipeline.

Besides concatenating FCS files this step also does arcsinh transformation. Conventionally we have used a co-factor of 5 for CyTOf and 150 for Flow data.

scr01_00_fcs_to_tsv.R

3. Run HDStIM, generate diagnostic plots, and run marker ranking function

scr02_00_run_hdstim_cytof.R

4. Export HDStIM statistics

scr04_00_export_hdstim_stats.R