97 lines (96 with data), 3.0 kB

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'