bioc-issue-bot
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2 hours ago Hi @AliYoussef96
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The DESCRIPTION file for this package is:
Package: LimROTS
Title: A Hybrid Method Integrating Empirical Bayes and
Reproducibility-Optimized Statistics for Robust Analysis of Proteomics
and Metabolomics Data
Version: 0.99.0
Authors@R:
c(person(given = "Ali", family = "Mostafa Anwar", role = c("aut", "cre"),
email= "aliali.mostafa99@gmail.com",
comment = c(ORCID = "0000-0002-5201-387X")),
person(given = "Leo", family = "Lahti", role = c("aut" ,"ths"),
email = "leo.lahti@iki.fi",
comment = c(ORCID = "0000-0001-5537-637X")),
person(given = "Akewak", family = "Jeba", role = c("aut","ctb"),
email = "akewak.k.jeba@utu.fi",
comment = c(ORCID = "0009-0007-1347-7552")),
person(given = "Eleanor", family = "Coffey", role = c("aut", "ths"),
email = "elecof@utu.fi",
comment = c(ORCID = "0000-0002-9717-5610")))
Description: 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.
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.4.0)
biocViews: Software, GeneExpression, DifferentialExpression,
Microarray, RNASeq, Proteomics, ImmunoOncology, Metabolomics, mRNAMicroarray
URL: https://github.com/AliYoussef96/LimROTS, https://aliyoussef96.github.io/LimROTS/
BugReports: https://github.com/AliYoussef96/LimROTS/issues
VignetteBuilder:
knitr
Imports:
limma,
parallel,
foreach,
doParallel,
stringr,
qvalue,
SummarizedExperiment,
utils,
stats,
doRNG,
dplyr
Suggests:
BiocStyle,
ggplot2,
magick,
testthat (>= 3.0.0),
knitr,
rmarkdown,
ROTS
Config/testthat/edition: 3
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