Google Colab interface to HDStIM (High Dimensional Stimulation Immune Mapping)

Abstract

HDStIM is a method for identifying responses to experimental stimulation in mass or flow cytometry that uses high dimensional analysis of measured parameters and can be performed with an end-to-end unsupervised approach. In the context of in vitro stimulation assays where high-parameter cytometry was used to monitor intracellular response markers, using cell populations annotated either through automated clustering or manual gating for a combined set of stimulated and unstimulated samples, 'HDStIM' labels cells as responding or non-responding. The package also provides auxiliary functions to rank intracellular markers based on their contribution to identifying responses and generating diagnostic plots.

Figure 1. Schematic outline for the use of multiple response markers by HDStIM to identify cells with a responding phenotype from unstimulated and stimulated experimental samples for a given stimulation - cell population combination.

Colab notebook

This notebook is an attempt to make it easier to use HDStIM. However, since it runs on Google Colab, it has its limitations. For example, uploading a large dataset is very slow and may not be straightforward. Also, the marker ranking function that utilizes multiple cores may be orders of magnitude slower than on a local machine with more than two cores. See the more information section at the bottom of the notebook on how to run this notebook locally (recommended).

Notebook	Link
ColabHDStIM.ipynb

Note: Under default settings, the notebook should be able to run an example dataset.

Helpful links

1. HDStIM related
   1. Documentation website: https://niaid.github.io/HDStIM/
   2. Source code: https://github.com/niaid/HDStIM/
   3. CRAN page: https://cran.r-project.org/package=HDStIM
2. Google colab related
   1. Google Colab frequently asked questions
   2. Welcome to Colab!
   3. Practical introduction to Google Colab for data science (YouTube video)

Citation

To cite ColabHDStIM:

• Rohit Farmer. (2022). ColabHDStIM: A Google Colab interface to HDStIM (High Dimensional Stimulation Immune Mapping) (v1.1.0). Zenodo. https://doi.org/10.5281/zenodo.7231731
• Rohit Farmer, Richard Apps, Juan Quiel, Brian Sellers, Foo Cheung, Jinguo Chen, Amrita Mukherjee, Peter McGuire, John S Tsang. (2022). Multiparameter stimulation mapping of signaling states in single pediatric immune cells reveals heightened tonic activation during puberty. bioRxiv 2022.11.14.516371. https://doi.org/10.1101/2022.11.14.516371