c(person("Elena", "Filatova", role=c("aut", "cre"), email="filatova@nniiem.ru"), person("Nikolai", "Sakharnov", role="dtc"), person("Dmitry", "Knyazev", role="dtc"), person("Oleg", "Utkin", role="dtc"), person("Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia", role="fnd"))
Set of functions designed to simplify transcriptome analysis and identification of marker molecules using microarrays data. The package includes a set of functions that allows performing full pipeline of analysis including data normalization, summarisation, binary classification, FDR multiple comparison and the definition of potential biological markers.
caret, gbm, genefilter, graphics, limma, preprocessCore, pROC,
stats, SQN
Elena Filatova [aut, cre],
Nikolai Sakharnov [dtc],
Dmitry Knyazev [dtc],
Oleg Utkin [dtc],
Blokhina Scientific Research Institute of Epidemiology and Microbiology
of Nizhny Novgorod, Russia [fnd]

Set of functions designed to simplify transcriptome analysis and identification of marker molecules using microarrays data. The package includes a set of functions that allows performing full pipeline of analysis including data normalization, summarisation, binary classification, FDR (False Discovery Rate) multiple comparison and the definition of potential biological markers.

Metabolomics-Based Models for Imputing Risk
c(person(given = "Daniele",
family = "Bizzarri",
role = c("aut", "cre"),
email = "d.bizzarri@lumc.nl",
comment = c(ORCID = "0000-0002-6881-273X")),
person(given = "Marcel",
family = "Reinders",
role = c("aut","ths"),
email = "m.j.t.reinders@tudelft.nl",
comment = c(ORCID = "0000-0002-1148-1562")),
person(given = "Marian",
family = "Beekman",
role = c("aut"),
email = "M.Beekman@lumc.nl",
comment = c(ORCID = "0000-0003-0585-6206")),
person(given = "Pieternella Eline",
family = "Slagboom",
role = c("aut","ths"),
email = "P.Slagboom@lumc.nl",
comment = c(ORCID = "0000-0002-2875-4723")),
person(given = "Erik",
family = "van den Akker",
role = c("aut","ths"),
email = "E.B.van_den_Akker@lumc.nl",
comment = c(ORCID = "0000-0002-7693-0728")))
Provides an intuitive framework for ad-hoc statistical analysis of 1H-NMR metabolomics by Nightingale Health. It allows to easily explore new metabolomics measurements assayed by Nightingale Health, comparing the distributions with a large Consortium (BBMRI-nl); project previously published metabolic scores [<doi:10.1016/j.ebiom.2021.103764>, <doi:10.1161/CIRCGEN.119.002610>, <doi:10.1038/s41467-019-11311-9>, <doi:10.7554/eLife.63033>, <doi:10.1161/CIRCULATIONAHA.114.013116>, <doi:10.1007/s00125-019-05001-w>]; and calibrate the metabolic surrogate values to a desired dataset.
caret, DT, foreach, ggplot2, glmnet, heatmaply, matrixStats,
pkgload, plotly, plyr, pROC, purrr, shiny, shinycssloaders,
shinyFiles, shinydashboard, shinyjs, shinyWidgets, stats,
survival, survminer, dplyr
Daniele Bizzarri [aut, cre] (<https://orcid.org/0000-0002-6881-273X>),
Marcel Reinders [aut, ths] (<https://orcid.org/0000-0002-1148-1562>),
Marian Beekman [aut] (<https://orcid.org/0000-0003-0585-6206>),
Pieternella Eline Slagboom [aut, ths]
(<https://orcid.org/0000-0002-2875-4723>),
Erik van den Akker [aut, ths] (<https://orcid.org/0000-0002-7693-0728>)