README.md

WhySingleCell

This repository contains the code and files for the calculations and figures from "Are we there yet? Assessing the readiness of single-cell proteomics to answer biological hypotheses"

File Information

• Figure_1ab.R: R script that produces Figure _1a.png and Figure_1b.png

• Classification - Number of Cells.ipynb: python notebook that produces the calculated numbers in the Classification - Number of Cells section of the paper

Recreating Figure 1

1. Run Figure_1ab.R

Recreating the Calculations

1. Unadjusted for Dropout: Run all cells in Classification - Number of Cells.ipynb
2. Adjusted for Dropout: In the first cell in Classification - Number of Cells.ipynb, set d = 1 and run all cells