ArticleBioinformatics (Oxford, England)2023
optima: an open-source R package for the Tapestri platform for integrative single cell multiomics data analysis.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- A single-cell multi-omics assay for simultaneous measurement of vector copy number and protein expression in CAR T cells.Molecular therapy. Advances · 2026Article
- Integrative modeling of read depth and B-allele frequency improves single-cell copy number calling from targeted DNA sequencing panels.bioRxiv : the preprint server for biology · 2026Article
- Integrative Modeling of Read Depth and B-Allele Frequency Improves Single-Cell Copy Number Calling from Targeted DNA Sequencing Panels.Computational and structural biotechnology journal · 2026Article
- scDNA: Single Cell DNA analysis software toolkit for subclonality discovery and assessment.bioRxiv : the preprint server for biology · 2025Article
- scafari: exploring scDNA-seq data.Bioinformatics (Oxford, England) · 2025Article
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Authors and funding
5 authors.
Funding
Abstract
summaryThe 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.