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| inst/doc | ||
| doc | ||
| Meta | ||
| Meta | ||
| Aux |
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| Package: DIscBIO | ||
| Date: 2020-05-04 | ||
| Date: 2020-07-30 | ||
| Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics | ||
| Version: 0.99.8 | ||
| 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")) | ||
| ) | ||
| 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. | ||
| <doi:10.1101/700989>. | ||
| biocViews: SingleCell, Transcriptomics, Clustering, DecisionTree | ||
| 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, biomaRt, samr, igraph, | ||
| RWeka, partykit, grid, philentropy, NetIndices, png, matrixStats, grDevices, | ||
| readr, RColorBrewer, ggplot2, rpart, fpc, cluster, rpart.plot, amap, dplyr, | ||
| tsne, AnnotationDbi, org.Hs.eg.db, calibrate, graphics, stats, utils | ||
| 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 | ||
| R (>= 4.0), SingleCellExperiment | ||
| Suggests: | ||
| knitr, | ||
| rmarkdown, | ||
| testthat, | ||
| enrichR, | ||
| Seurat | ||
| VignetteBuilder: knitr | ||
| Seurat | ||
| LazyData: true | ||
| RoxygenNote: 7.1.0 | ||
| 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-FindOutliersKM.R' | ||
| 'DIscBIO-generic-FindOutliersMB.R' | ||
| 'DIscBIO-generic-KMClustDiffGenes.R' | ||
| 'DIscBIO-generic-KMclustheatmap.R' | ||
| 'DIscBIO-generic-KmeanOrder.R' | ||
| 'DIscBIO-generic-MBClustDiffGenes.R' | ||
| 'DIscBIO-generic-MBclustheatmap.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-comptsneMB.R' | ||
| 'DIscBIO-generic-plotExptSNE.R' | ||
| 'DIscBIO-generic-plotGap.R' | ||
| 'DIscBIO-generic-plotKmeansLabelstSNE.R' | ||
| 'DIscBIO-generic-plotMBLabelstSNE.R' | ||
| 'DIscBIO-generic-plotOrderKMtsne.R' | ||
| 'DIscBIO-generic-plotOrderMBtsne.R' | ||
| 'DIscBIO-generic-plotLabelstSNE.R' | ||
| 'DIscBIO-generic-plotOrderTsne.R' | ||
| 'DIscBIO-generic-plotSilhouette.R' | ||
| 'DIscBIO-generic-plotSymbolstSNE.R' | ||
| 'DIscBIO-generic-plotexptsneMB.R' | ||
| 'DIscBIO-generic-plotsilhouetteMB.R' | ||
| 'DIscBIO-generic-plottSNE.R' | ||
| 'DIscBIO-generic-plottsneMB.R' | ||
| 'DIscBIO-generic-pseudoTimeOrdering.R' | ||
| 'J48DT.R' | ||
| 'J48DTeval.R' | ||
| 'Jaccard.R' | ||
| 'MB_Order.R' | ||
| 'NetAnalysis.R' | ||
| 'Networking.R' | ||
| 'PPI.R' | ||
| 'PlotMBexpPCA.R' | ||
| 'PlotMBorderPCA.R' | ||
| 'PlotMBpca.R' | ||
| 'RpartDT.R' | ||
| 'RpartEVAL.R' | ||
| 'VolcanoPlot.R' | ||
| 'customConverters.R' | ||
| 'datasets.R' | ||
| 'retrieveBiomart.R' | ||
| 'internal-functions.R' | ||
| 'prepExampleDataset.R' | ||
| 'reformatSiggenes.R' | ||
| 'replaceDecimals.R' | ||
| 'samr-adapted.R' |
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| Original file line number | Diff line number | Diff line change |
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| MIT License | ||
|
|
||
| Copyright (c) 2019 SystemsBiologist | ||
|
|
||
| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
|
|
||
| The above copyright notice and this permission notice shall be included in all | ||
| copies or substantial portions of the Software. | ||
|
|
||
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| SOFTWARE. | ||
| YEAR: 2019 | ||
| COPYRIGHT HOLDER: Salim Ghannoum |
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