LimROTS
This is thereleased version of LimROTS; for the devel version, seeLimROTS.
LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis
Bioconductor version: Release (3.22)
Differential expression analysis is a prevalent method utilised in the examination of diverse biological data. The reproducibility-optimized test statistic (ROTS) modifies a t-statistic based on the data's intrinsic characteristics and ranks features according to their statistical significance for differential expression between two or more groups (f-statistic). Focussing on proteomics and metabolomics, the current ROTS implementation cannot account for technical or biological covariates such as MS batches or gender differences among the samples. Consequently, we developed LimROTS, which employs a reproducibility-optimized test statistic utilising the limma methodology to simulate complex experimental designs. LimROTS is a hybrid method integrating empirical bayes and reproducibility-optimized statistics for robust analysis of proteomics and metabolomics data.
Author: Ali Mostafa Anwar [aut, cre]
ORCID: 0000-0002-5201-387X, Leo Lahti [aut, ths] ORCID: 0000-0001-5537-637X, Akewak Jeba [aut, ctb] ORCID: 0009-0007-1347-7552, Eleanor Coffey [aut, ths] ORCID: 0000-0002-9717-5610
Maintainer: Ali Mostafa Anwar <aliali.mostafa99 at gmail.com>
citation("LimROTS")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("LimROTS")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("LimROTS")| LimROTS | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression,GeneExpression,ImmunoOncology,Metabolomics,Microarray,Proteomics,RNASeq,Software,mRNAMicroarray |
| Version | 1.2.8 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 4.5.0),SummarizedExperiment |
| Imports | limma,stringr,qvalue, utils, stats,BiocParallel,S4Vectors,dplyr |
| System Requirements | |
| URL | https://github.com/AliYoussef96/LimROTShttps://aliyoussef96.github.io/LimROTS/ |
| Bug Reports | https://github.com/AliYoussef96/LimROTS/issues |
See More
| Suggests | BiocStyle,ggplot2,magick,testthat (>= 3.0.0),knitr,rmarkdown,caret,ROTS |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | LimROTS_1.2.8.tar.gz |
| Windows Binary (x86_64) | LimROTS_1.1.4.zip |
| macOS Binary (x86_64) | LimROTS_1.2.8.tgz |
| macOS Binary (arm64) | LimROTS_1.2.8.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/LimROTS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/LimROTS |
| Bioc Package Browser | https://code.bioconductor.org/browse/LimROTS/ |
| Package Short Url | https://bioconductor.org/packages/LimROTS/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.22 | Source Archive |