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Cell-Type-Specific Power Assessment

Bioconductor version: Release (3.19)

CYPRESS is a cell-type-specific power tool. This package aims to perform power analysis for the cell-type-specific data. It calculates FDR, FDC, and power, under various study design parameters, including but not limited to sample size, and effect size. It takes the input of a SummarizeExperimental(SE) object with observed mixture data (feature by sample matrix), and the cell-type mixture proportions (sample by cell-type matrix). It can solve the cell-type mixture proportions from the reference free panel from TOAST and conduct tests to identify cell-type-specific differential expression (csDE) genes.

Author: Shilin Yu [aut, cre] , Guanqun Meng [aut], Wen Tang [aut]

Maintainer: Shilin Yu <sy597 at>

Citation (from within R, enter citation("cypress")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

cypress Package User's Guide HTML R Script
Reference Manual PDF


biocViews DataImport, GeneExpression, RNASeq, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-2 | GPL-3
Depends R (>= 4.4.0)
Imports stats, abind, sirt, MASS, TOAST, tibble, parallel, preprocessCore, SummarizedExperiment, TCA, PROPER, methods, dplyr, utils, RColorBrewer, graphics, edgeR, BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071
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Suggests knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics, BiocManager, BiocStyle, Biobase
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Follow Installation instructions to use this package in your R session.

Source Package cypress_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64) cypress_1.0.0.tgz
macOS Binary (arm64) cypress_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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