optima: an open-source R package for the Tapestri platform for integrative single cell multiomics data analysis

Area of Science:

• Single-cell multi-omics analysis
• Computational biology and bioinformatics
• Cancer research and immunology

Background:

• The Tapestri platform enables simultaneous DNA and protein analysis at the single-cell level.
• Analyzing multi-modal single-cell data is crucial for understanding complex biological systems, such as heterogeneous tumor microenvironments.
• Existing tools may not fully address the specific needs of processing and integrating Tapestri-generated data.

Purpose of the Study:

• To introduce optima, an R package designed for the comprehensive processing and analysis of single-cell DNA and protein data from the Tapestri platform.
• To provide a streamlined workflow for data filtering, integration, normalization, transformation, and visualization.
• To facilitate the identification of distinct cell populations and the characterization of surface protein expression patterns.

Main Methods:

• Development of an R package, "optima", leveraging established bioinformatics pipelines.
• Implementation of functions for quality control, data integration, and normalization of multi-modal single-cell data.
• Inclusion of visualization tools for exploring cell populations and protein expression profiles.

Main Results:

• The optima package offers efficient and integrated analysis of Tapestri DNA and protein data.
• Users can effectively identify unique cell subsets within heterogeneous samples.
• The package enables the discovery of cell-specific surface protein expression patterns.

Conclusions:

• optima provides a valuable computational tool for researchers utilizing the Tapestri platform.
• The package enhances the ability to gain deeper insights into cellular heterogeneity and dynamics.
• optima supports the elucidation of complex biological processes at the single-cell level.