c(person("Rafael", "de Andrade Moral", role = c("aut", "cre"), email = "rafael.deandrademoral@mu.ie"), person("John", "Connolly", role = "aut"), person("Rishabh", "Vishwakarma", role = "ctb"), person("Caroline", "Brophy", role = "aut"))
Rafael de Andrade Moral [aut, cre],
John Connolly [aut],
Rishabh Vishwakarma [ctb],
Caroline Brophy [aut]
methods, graphics, stats, utils, hnp, rootSolve, multcomp

A User-Friendly Pipeline for Biomarker Discovery in Single-Cell
Transcriptomics
c(
person(
given = "Salim",
family = "Ghannoum",
role = c("aut", "cph"),
email = "salim.ghannoum@medisin.uio.no"
),
person(
given = "Alvaro",
family = "Köhn-Luque",
role = c("aut", "ths"),
email = "alvaro.kohn-luque@medisin.uio.no"
),
person(
given = "Waldir",
family = "Leoncio",
role = c("cre", "aut"),
email = "w.l.netto@medisin.uio.no"
),
person(
given = "Damiano",
family = "Fantini",
role = c("ctb")
)
)
An open, multi-algorithmic pipeline for easy, fast and efficient
analysis of cellular sub-populations and the molecular signatures that
characterize them. The pipeline consists of four successive steps: data
pre-processing, cellular clustering with pseudo-temporal ordering, defining
differential expressed genes and biomarker identification. This package
implements extensions of the work published by Ghannoum et. al. (2019)
<doi:10.1101/700989>.
methods, TSCAN, boot, httr, mclust, statmod, igraph, RWeka,
philentropy, NetIndices, png, grDevices, readr, RColorBrewer,
ggplot2, rpart, fpc, cluster, rpart.plot, tsne, AnnotationDbi,
org.Hs.eg.db, graphics, stats, utils, impute
'DIscBIO-classes.R' 'DIscBIO-generic-ClassVectoringDT.R'
'DIscBIO-generic-ClustDiffGenes.R' 'DIscBIO-generic-Clustexp.R'
'DIscBIO-generic-DEGanalysis.R'
'DIscBIO-generic-DEGanalysis2clust.R'
'DIscBIO-generic-Exprmclust.R'
'DIscBIO-generic-FinalPreprocessing.R'
'DIscBIO-generic-FindOutliers.R'
'DIscBIO-generic-NoiseFiltering.R'
'DIscBIO-generic-Normalizedata.R'
'DIscBIO-generic-PCAplotSymbols.R'
'DIscBIO-generic-PlotmclustMB.R'
'DIscBIO-generic-clusteringOrder.R'
'DIscBIO-generic-clustheatmap.R' 'DIscBIO-generic-comptSNE.R'
'DIscBIO-generic-plotExptSNE.R' 'DIscBIO-generic-plotGap.R'
'DIscBIO-generic-plotLabelstSNE.R'
'DIscBIO-generic-plotOrderTsne.R'
'DIscBIO-generic-plotSilhouette.R'
'DIscBIO-generic-plotSymbolstSNE.R'
'DIscBIO-generic-plottSNE.R'
'DIscBIO-generic-pseudoTimeOrdering.R' 'J48DT.R' 'J48DTeval.R'
'Jaccard.R' 'NetAnalysis.R' 'Networking.R' 'PPI.R'
'PlotMBpca.R' 'RpartDT.R' 'RpartEVAL.R' 'VolcanoPlot.R'
'customConverters.R' 'datasets.R' 'internal-functions.R'
'prepExampleDataset.R' 'reformatSiggenes.R' 'replaceDecimals.R'
'samr-adapted.R'
Salim Ghannoum [aut, cph],
Alvaro Köhn-Luque [aut, ths],
Waldir Leoncio [cre, aut],
Damiano Fantini [ctb]