RnaSeqSampleSize
This package is for version 3.24 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RnaSeqSampleSize.
RnaSeqSampleSize
Bioconductor version: Development (3.24)
RnaSeqSampleSize package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data. It controls FDR for multiple testing and utilizes the average read count and dispersion distributions from real data to estimate a more reliable sample size. It is also equipped with several unique features, including estimation for interested genes or pathway, power curve visualization, and parameter optimization.
Author: Shilin Zhao Developer [aut, cre], Chung-I Li [aut], Yan Guo [aut], Quanhu Sheng [aut], Yu Shyr [aut]
Maintainer: Shilin Zhao Developer <zhaoshilin at gmail.com>
citation("RnaSeqSampleSize")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("RnaSeqSampleSize")
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("RnaSeqSampleSize")| RnaSeqSampleSize: Sample size estimation by real data | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ExperimentalDesign, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software |
| Version | 2.23.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 4.0.0), ggplot2, RnaSeqSampleSizeData |
| Imports | biomaRt, edgeR, heatmap3, matlab, KEGGREST, methods, grDevices, graphics, stats, Rcpp (>= 0.11.2), recount, ggpubr, SummarizedExperiment, tidyr, dplyr, tidyselect, utils |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, testthat |
| Linking To | Rcpp |
| 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 | RnaSeqSampleSize_2.23.0.tar.gz |
| Windows Binary (x86_64) | RnaSeqSampleSize_2.23.0.zip |
| macOS Binary (big-sur-x86_64) | RnaSeqSampleSize_2.23.0.tgz |
| macOS Binary (sonoma-arm64) | RnaSeqSampleSize_2.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RnaSeqSampleSize |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RnaSeqSampleSize |
| Bioc Package Browser | https://code.bioconductor.org/browse/RnaSeqSampleSize/ |
| Package Short Url | https://bioconductor.org/packages/RnaSeqSampleSize/ |
| Package Downloads Report | Download Stats |