Package: DIscBIO
Date: 2021-04-28
Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell
        Transcriptomics
Version: 1.2.0
Authors@R: 
	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")
		)
	)
Description: 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. More details on
	Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements
	extensions of the work published by Ghannoum et. al. (2019)
	<doi:10.1101/700989>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: methods, TSCAN, boot, httr, mclust, statmod, igraph, RWeka,
        philentropy, NetIndices, png, grDevices, RColorBrewer, ggplot2,
        rpart, fpc, cluster, rpart.plot, tsne, AnnotationDbi,
        org.Hs.eg.db, graphics, stats, utils, impute
Depends: R (>= 4.0), SingleCellExperiment
Suggests: testthat, Seurat
LazyData: true
RoxygenNote: 7.1.1
URL: https://github.com/ocbe-uio/DIscBIO
BugReports: https://github.com/ocbe-uio/DIscBIO/issues
Collate: '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-samr-adapted.R' 'internal-functions.R'
NeedsCompilation: no
Packaged: 2021-04-28 05:48:21 UTC; waldir
Author: Salim Ghannoum [aut, cph],
  Alvaro Köhn-Luque [aut, ths],
  Waldir Leoncio [cre, aut],
  Damiano Fantini [ctb]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Repository: CRAN
Date/Publication: 2021-04-28 07:00:06 UTC
Built: R 4.0.5; ; 2022-04-21 10:32:20 UTC; windows
