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RnaSeqSampleSize

This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RnaSeqSampleSize.

RnaSeqSampleSize


Bioconductor version: Development (3.19)

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 (from within R, enter citation("RnaSeqSampleSize")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, ExperimentalDesign, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 2.13.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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
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Suggests BiocStyle, knitr, testthat
Linking To Rcpp
Enhances
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Package Archives

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

Source Package RnaSeqSampleSize_2.13.0.tar.gz
Windows Binary RnaSeqSampleSize_2.13.0.zip
macOS Binary (x86_64) RnaSeqSampleSize_2.13.0.tgz
macOS Binary (arm64) RnaSeqSampleSize_2.13.0.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/
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