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'