RnaSeqSampleSize

DOI: 10.18129/B9.bioc.RnaSeqSampleSize    

This package is for version 3.15 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RnaSeqSampleSize.

RnaSeqSampleSize

Bioconductor version: Release (3.15)

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	2.6.0
In Bioconductor since	BioC 3.1 (R-3.2) (7.5 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
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RnaSeqSampleSize_2.6.0.tar.gz
Windows Binary	RnaSeqSampleSize_2.6.0.zip
macOS Binary (x86_64)	RnaSeqSampleSize_2.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RnaSeqSampleSize
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RnaSeqSampleSize
Package Short Url	https://bioconductor.org/packages/RnaSeqSampleSize/
Package Downloads Report	Download Stats