ERSSA
This is the released version of ERSSA; for the devel version, see ERSSA.
Empirical RNA-seq Sample Size Analysis
Bioconductor version: Release (3.23)
The ERSSA package takes user supplied RNA-seq differential expression dataset and calculates the number of differentially expressed genes at varying biological replicate levels. This allows the user to determine, without relying on any a priori assumptions, whether sufficient differential detection has been acheived with their RNA-seq dataset.
Author: Zixuan Shao [aut, cre]
Maintainer: Zixuan Shao <Zixuanshao.zach at gmail.com>
citation("ERSSA")):
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")
BiocManager::install("ERSSA")
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("ERSSA")| ERSSA Package Introduction | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, MultipleComparison, QualityControl, RNASeq, Software, Transcription |
| Version | 1.30.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL-3 | file LICENSE |
| Depends | R (>= 4.0.0) |
| Imports | edgeR(>= 3.23.3), DESeq2(>= 1.21.16), ggplot2 (>= 3.0.0), RColorBrewer (>= 1.1-2), plyr (>= 1.8.4), BiocParallel(>= 1.15.8), apeglm(>= 1.4.2), grDevices, stats, utils |
| System Requirements | |
| URL | https://github.com/zshao1/ERSSA |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| 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 | ERSSA_1.30.0.tar.gz |
| Windows Binary (x86_64) | ERSSA_1.30.0.zip |
| macOS Binary (big-sur-x86_64) | ERSSA_1.30.0.tgz |
| macOS Binary (sonoma-arm64) | ERSSA_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ERSSA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ERSSA |
| Bioc Package Browser | https://code.bioconductor.org/browse/ERSSA/ |
| Package Short Url | https://bioconductor.org/packages/ERSSA/ |
| Package Downloads Report | Download Stats |