LimROTS
This is the released version of LimROTS; for the devel version, see LimROTS.
LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis
Bioconductor version: Release (3.23)
Differential expression analysis is commonly used to study diverse biological datasets. The reproducibility-optimized test statistic (ROTS) (Elo et al., 2008, <doi:10.1109/tcbb.2007.1078>) uses a modified t-statistic to prioritise features that differ between two or more groups. However, the ROTS Bioconductor implementation (Suomi et al., 2017, <doi:10.1371/journal.pcbi.1005562>) did not accommodate technical or biological covariates. LimROTS (Anwar et al., 2025, <doi:10.1093/bioinformatics/btaf570>) addressed this limitation by combining a reproducibility-optimized test statistic with the limma empirical Bayes approach (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>). This enables the analysis of more complex experimental designs and the incorporation of covariates.
Author: Ali Mostafa Anwar [aut, cre] 
, Leo Lahti [aut, ths] , Akewak Jeba [aut, ctb] , Eleanor Coffey [aut, ths] , Rasmus Hindström [ctb]
Maintainer: Ali Mostafa Anwar <aliali.mostafa99 at gmail.com>
citation("LimROTS")):Ali Mostafa Anwar, Leo Lahti, Akewak Jeba, Eleanor Coffey. LimROTS: LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis. doi:10.18129/B9.bioc.LimROTS, R package version 1.4.0, https://bioconductor.org/packages/LimROTS.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("LimROTS")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("LimROTS")| LimROTS: Survival Analysis with Cox and Competing Risks Models | HTML | R Script |
| LimROTS: Overview and Differential Expression Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, Metabolomics, Microarray, Proteomics, RNASeq, Software, mRNAMicroarray |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 4.5.0), SummarizedExperiment |
| Imports | limma, stringr, qvalue, utils, stats, BiocParallel, S4Vectors, dplyr, survival, cmprsk, variancePartition |
| System Requirements | |
| URL | https://github.com/AliYoussef96/LimROTS https://aliyoussef96.github.io/LimROTS/ |
| Bug Reports | https://github.com/AliYoussef96/LimROTS/issues |
See More
| Suggests | BiocStyle, ggplot2, testthat (>= 3.0.0), knitr, rmarkdown, caret, ROTS, mia, miaTime, TreeSummarizedExperiment |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | LimROTS_1.4.0.tar.gz |
| Windows Binary (x86_64) | LimROTS_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | LimROTS_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | LimROTS_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/LimROTS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/LimROTS |
| Package Short Url | https://bioconductor.org/packages/LimROTS/ |
| Package Downloads Report | Download Stats |