cypress

CYPRESS performs power analysis for cell-type-specific data, calculating FDR, FDC, and power under various study design parameters to identify cell-type-specific differential expression (csDE) genes.

Key Features:

• Power Analysis: Calculates FDR, FDC, and power under various study design parameters including sample size and effect size.
• Cell-Type Mixture Proportion Estimation: Solves cell-type mixture proportions from the reference-free panel from TOAST.
• csDE Gene Identification: Conducts tests to identify cell-type-specific differential expression (csDE) genes.
• SummarizedExperiment Input: Accepts a SummarizedExperiment (SE) object with observed mixture data (feature by sample matrix) and cell-type mixture proportions (sample by cell-type matrix).

Scientific Applications:

• Cell-Type-Specific Differential Expression Studies: Enables power assessment and detection of cell-type-specific differential expression genes from mixture data.

Methodology:

CYPRESS takes as input a SummarizedExperiment (SE) object containing observed mixture data (feature by sample matrix) and cell-type mixture proportions (sample by cell-type matrix), and can solve cell-type mixture proportions from the reference-free panel from TOAST.