cypress

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see cypress.

Cell-Type-Specific Power Assessment


Bioconductor version: 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 georgetown.edu>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cypress")

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

Documentation

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

browseVignettes("cypress")
cypress Package User's Guide HTML R Script
Reference Manual PDF
NEWS Text

Details

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
System Requirements
URL https://github.com/renlyly/cypress
Bug Reports https://github.com/renlyly/cypress/issues
See More
Suggests knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics, BiocManager, BiocStyle, Biobase
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cypress_1.0.0.tar.gz
Windows Binary (x86_64) cypress_1.0.0.zip
macOS Binary (x86_64) cypress_1.0.0.tgz
macOS Binary (arm64) cypress_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cypress
Source Repository (Developer Access) git clone [email protected]:packages/cypress
Bioc Package Browser https://code.bioconductor.org/browse/cypress/
Package Short Url https://bioconductor.org/packages/cypress/
Package Downloads Report Download Stats