Package: DIscBIO
Date: 2023-11-06
Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell
        Transcriptomics
Version: 1.2.2
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, httr, mclust, statmod, igraph, RWeka, vegan,
        NetIndices, png, grDevices, RColorBrewer, ggplot2, rpart, fpc,
        cluster, rpart.plot, tsne, AnnotationDbi, org.Hs.eg.db,
        graphics, stats, utils, impute, withr
Depends: R (>= 4.0), SingleCellExperiment
Suggests: testthat, Seurat
LazyData: true
RoxygenNote: 7.2.3
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'
        'bootstrap.R' 'calc_pcareduceres.R' 'cross.val.R'
        'customConverters.R' 'datasets.R'
        'internal-functions-samr-adapted.R' 'internal-functions.R'
NeedsCompilation: no
Packaged: 2023-11-06 09:18:46 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: 2023-11-06 10:50:02 UTC
Built: R 4.3.3; ; 2025-04-07 02:24:06 UTC; windows
