Abstract
Background: In single cell DNA and RNA sequencing experiments, the number of cells to sequence must be decided before running an experiment, and afterwards, it is necessary to decide whether sufficient cells were sampled. These questions can be addressed by calculating the probability of sampling at least a defined number of cells from each subpopulation (cell type or cancer clone). Results: We developed an interactive web application called SCOPIT (Single-Cell One-sided Probability Interactive Tool), which calculates the required probabilities using a multinomial distribution (www.navinlab.com/SCOPIT). In addition, we created an R package called pmultinom for scripting these calculations. Conclusions: Our tool for fast multinomial calculations provide a simple and intuitive procedure for prospectively planning single-cell experiments or retrospectively evaluating if sufficient numbers of cells have been sequenced. The web application can be accessed at navinlab.com/SCOPIT.
| Original language | English (US) |
|---|---|
| Article number | 193167 |
| Journal | BMC bioinformatics |
| Volume | 20 |
| Issue number | 1 |
| DOIs | |
| State | Published - Nov 12 2019 |
Funding
This work was supported by grants to NN from the American Cancer Society (129098-RSG-16-092-01-TBG), the Chan-Zuckerberg Initiative Human Cell Atlas Seed Network Grant (HCA3–0000000147) and the CPRIT Single Cell Genomics Center Grant (RP180684). This work was also supported by Susan Komen (PDF17487910) and AACR Basic Cancer Research Fellowships (174042GAO) to RG. AD was supported by an NLM fellowship (4T15LM007093–25). These funding agencies did not play any role in the design of the study, the collection, analysis, and interpretation of data, or in the writing of the manuscript.
Keywords
- Multinomial distributions
- Sample size
- Single cell sequencing
ASJC Scopus subject areas
- Structural Biology
- Biochemistry
- Molecular Biology
- Computer Science Applications
- Applied Mathematics
