RnaSeqSampleSize
This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RnaSeqSampleSize.
RnaSeqSampleSize
Bioconductor version: Release (3.17)
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")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 2.10.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (8.5 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 |
| Linking To | Rcpp |
| Suggests | BiocStyle, knitr, testthat |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RnaSeqSampleSize_2.10.0.tar.gz |
| Windows Binary | RnaSeqSampleSize_2.10.0.zip |
| macOS Binary (x86_64) | RnaSeqSampleSize_2.10.0.tgz |
| macOS Binary (arm64) | RnaSeqSampleSize_2.10.0.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 |