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DESCRIPTION
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DESCRIPTION
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Package: DIscBIO
Date: 2020-07-30
Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
Version: 1.0.0
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. 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,
readr, 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#usage
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.R'
'prepExampleDataset.R'
'reformatSiggenes.R'
'replaceDecimals.R'
'samr-adapted.R'