Summary

The Tapestri platform offers DNA and protein analysis at the single-cell level. Integrating both types of data is beneficial for studying multiple cell populations in heterogeneous microenvironments, such as tumor tissues. Here, we present optima, an R package for the processing and analysis of data generated from the Tapestri platform. This package provides streamlined functionality for raw data filtering, integration, normalization, transformation, and visualization. Insights gained from the optima package help users to identify unique cell populations and uncover surface protein expression patterns. The results generated by optima help researchers elucidate dynamic changes at the single-cell level in heterogeneous microenvironments.

Availability and implementation

This package is available in Github: https://github.com/rachelgriffard/optima.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.