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("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 | ||
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 |