For each cell phenotype of interest, the fraction of that cell phenotype in proportion to all of the cells in that sample will be quantified as: $phenotype/all\ cells$.

For biomarker positivity annotations, the fraction of each relevant cell type that is positive for that biomarker within each sample will also be quantified as: $biomarker\ positive/(biomarker\ positive + biomarker\ negative)$

If a metadata trait specifying cohort definitions is provided, the result of a statistical comparison between groups will also be reported for each of these cell frequencies:

• For cohort definitions with two groups, the result of a two sample t-test will be reported.
• For cohort definitions with more than two groups, the result of a one-way ANOVA will be reported, with a Tukey’s post-hoc test performed to identify significant pairwise differences following significant ANOVA results.
• All reported p-values will be corrected for multiple hypotheses using a Benjamini-Hochberg correction.