cypress
This is the development version of cypress; for the stable release version, see cypress.
Cell-Type-Specific Power Assessment
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Shilin Yu <sy597 at georgetown.edu>
citation("cypress")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneExpression, RNASeq, Sequencing, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/cypress |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cypress |
| Bioc Package Browser | https://code.bioconductor.org/browse/cypress/ |
| Package Short Url | https://bioconductor.org/packages/cypress/ |
| Package Downloads Report | Download Stats |