RnaSeqSampleSize

DOI: 10.18129/B9.bioc.RnaSeqSampleSize  

This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RnaSeqSampleSize.

RnaSeqSampleSize

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	RnaSeqSampleSize: Sample size estimation by real data
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, ExperimentalDesign, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version	2.8.0
In Bioconductor since	BioC 3.1 (R-3.2) (8 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
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL
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_2.8.0.tar.gz
Windows Binary	RnaSeqSampleSize_2.8.0.zip
macOS Binary (x86_64)	RnaSeqSampleSize_2.8.0.tgz
macOS Binary (arm64)	RnaSeqSampleSize_2.8.0.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