cypress
This is the released version of cypress; for the devel version, see cypress.
Cell-Type-Specific Power Assessment
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 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_1.8.0.tar.gz |
| Windows Binary (x86_64) | cypress_1.8.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | cypress_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | cypress_1.8.0.tgz |
| 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 |