bioc-issue-bot
commented
3 years ago Hi @lievenclement
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: msqrob2
Title: Robust statistical inference for quantitative LC-MS proteomics
Version: 0.99.1
Authors@R: c(
person(given = "Lieven",
family = "Clement",
role = c("aut", "cre"),
email = "lieven.clement@ugent.be",
comment = c(ORCID = "0000-0002-9050-4370")),
person(given = "Laurent",
family = "Gatto",
role = c("aut"),
email = "laurent.gatto@uclouvain.be",
comment = c(ORCID = "0000-0002-1520-2268")),
person(family = "Crook",
given = "Oliver M.",
email = "oliver.crook@stats.ox.ac.uk",
comment = c(ORCID = "0000-0001-5669-8506"),
role = "aut"),
person(given = "Adriaan",
family = "Sticker",
email = "adriaan.sticker@ugent.be",
role = "ctb"),
person(given = "Ludger",
family = "Goeminne",
email = " ludgergoeminne@gmail.com",
role = "ctb"))
Description: msqrob2 provides a robust linear mixed model framework for assessing differential abundance in
MS-based Quantitative proteomics experiments. Our workflows can start from raw peptide intensities or
summarised protein expression values. The model parameter estimates can be stabilized by ridge regression,
empirical Bayes variance estimation and robust M-estimation. msqrob2's hurde workflow can handle missing
data without having to rely on hard-to-verify imputation assumptions, and, outcompetes state-of-the-art
methods with and without imputation for both high and low missingness. It builds on QFeature infrastructure
for quantitative mass spectrometry data to store the model results together with the raw data and preprocessed
data.
Depends:
R (>= 4.0),
QFeatures (>= 1.1.2)
Imports:
stats,
methods,
lme4,
purrr,
BiocParallel,
Matrix,
MASS,
limma,
SummarizedExperiment,
codetools
Suggests:
multcomp,
gridExtra,
knitr,
BiocStyle,
RefManageR,
sessioninfo,
rmarkdown,
testthat,
tidyverse,
plotly,
msdata,
MSnbase,
matrixStats,
MsCoreUtils
License: Artistic-2.0
Collate: 'msqrob-framework.R' 'allGenerics.R'
'accessors.R' 'msqrob.R' 'msqrob-utils.R' 'StatModel-methods.R'
'hypothesisTest-methods.R' 'msqrob-methods.R' 'msqrobAggregate.R'
'topFeatures.R' 'data.R' 'msqrobQB.R' 'msqrobHurdle-methods.R'
Encoding: UTF-8
VignetteBuilder: knitr
Roxygen: list(markdown=TRUE)
RoxygenNote: 7.1.1
biocViews:
Proteomics,
MassSpectrometry,
DifferentialExpression,
MultipleComparison,
Regression,
ExperimentalDesign,
Software,
ImmunoOncology,
Normalization,
TimeCourse,
Preprocessing
lievenclement
nturaga
vjcitn
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