Files in stela2502/BioData

The package allows to annotate a numeric data.table with col and row data

NEWS.md R/000_EXTERNAL_heatmap.3.R R/001_data_files.R R/01.class.BioData.R R/021_loadObj.R R/022_saveObj.R R/02_collaps.R R/02_reorder.obj.R R/CodonHeatmap.R R/CreateBin.R R/DimReduction.R R/Get_PartialTest_Obj.R R/IdentifyMarkerGenes.R R/Make3D4Obj.R R/PartialTests.R R/Plots_vioplot.R R/RcppExports.R R/SQLite_ExpressionSummary.R R/SQLite_SampleSummary.R R/SeuratVarGenes.R R/Seurat_FindAllMarkers.R R/Split4Geo.R R/addCellCyclePhase.R R/add_to_stat.R R/as.R R/as_BioData.R R/as_CellexalvrR.R R/as_Seurat.R R/as_cellexalvr.R R/as_loom2BioData.R R/auto_order_grouping.R R/auto_reorder_grouping.R R/bestGrouping.R R/changeNames.R R/cleanUpGroup.R R/clusters.R R/clusters_gene.R R/collapse.R R/collapse2codons.R R/colnames.R R/color_4.R R/combineGroupings.R R/complexHeatmap.R R/convert_to.R R/copy_grouping.R R/copy_mds_objects.R R/createDuplicates.R R/createStats.R R/dataframe2biodata.R R/defineGOIs.R R/defineHeatmapColors.R R/define_grouping.R R/definition.R R/export.data.R R/extractCodonInformation.R R/filterGenes.R R/findDuplicates.R R/findOverlapWithCells.R R/fit_4_rf.R R/force.numeric.R R/get.genes.cor.to.R R/getEnsembl.R R/getGeneInfo.R R/getGenesExpressedHigherThanExpected.R R/getNgenesFromMultiGroupStats.R R/getSymbols.R R/getTopSigGenes.R R/group_intersect_order.R R/groups.boxplot.R R/heatPlotTimelines2D.R R/load_CellexalVR_selection.R R/log.R R/logThis.R R/mds.R R/merge.R R/merge_cells.R R/normalize.R R/ontologyLogPage.R R/plot.codonUsage.R R/plot.legend.R R/plot2col_barplot.R R/plotMDS.R R/plot_velocyto.R R/positivesOnly.R R/preprocess.R R/pseudotimeTest.R R/pseudotimeTest3D.R R/pwd.R R/quality_of_fit.R R/readLoomFile.R R/reduceTo.R R/removeNeg.R R/renew.R R/reorder_grouping.R R/reorder_on_wilcox_results.R R/rfCluster_col.R R/rfCluster_row.R R/rownames.R R/runStats_inThread.R R/sampleCodonUsage.R R/simpleAnova.R R/stat_table.R R/tRF.typeHeatmap.R R/tRNA_stats.R R/transpose.R R/useInbuiltGOIlists.R R/z.score.R README.md install.R logfile.R man/CellCycle.Rd man/CellCycleGenes.Rd man/CodonHeatmap-methods.Rd man/Cpp_FindAllMarkers-methods.Rd man/CreateBin-methods.Rd man/DimReduction.Rd man/Epigenetic.Rd man/Get_PartialTest_Obj-methods.Rd man/H5Anno2df-methods.Rd man/IdentifyMarkerGenes-methods.Rd man/Make3D4obj-methods.Rd man/MicroArray.Rd man/PartialTests-methods.Rd man/SQLite_ExpressionSummary-methods.Rd man/SQLite_SampleSummary-methods.Rd man/SeuratVarGenes-methods.Rd man/Seurat_FindAllMarkers-methods.Rd man/SingleCells.Rd man/Split4Geo-methods.Rd man/TestData.Rd man/addCellCyclePhase-methods.Rd man/add_to_stat-methods.Rd man/as_BioData-methods.Rd man/as_BioData.Rd man/as_Seurat-methods.Rd man/as_cellexalvr-methods.Rd man/as_cellexalvr.Rd man/auto_order_grouping-methods.Rd man/auto_reorder_grouping-methods.Rd man/bestGrouping.Rd man/changeNames-methods.Rd man/cleanUpGroup-methods.Rd man/clusters-methods.Rd man/clusters_gene-methods.Rd man/collaps-methods.Rd man/collapse-methods.Rd man/collapse2codons-methods.Rd man/colnames-methods.Rd man/colors_4-methods.Rd man/combineGroupings-methods.Rd man/complexHeatmap-methods.Rd man/convert_to-methods.Rd man/copy_grouping-methods.Rd man/copy_mds_objects-methods.Rd man/createDuplicates-methods.Rd man/createRFgrouping_col-methods.Rd man/createRFgrouping_row-methods.Rd man/createStats-methods.Rd man/dataframe2biodata-methods.Rd man/defineGOIs-methods.Rd man/defineHeatmapColors-methods.Rd man/define_grouping-methods.Rd man/export.data-methods.Rd man/extractCodonInformation-methods.Rd man/filterGenes-methods.Rd man/findDuplicates-methods.Rd man/findOverlapWithCells-methods.Rd man/fit_4_rf-methods.Rd man/force.numeric-methods.Rd man/get.genes.cor.to-methods.Rd man/getEnsembl-methods.Rd man/getGeneInfo-methods.Rd man/getGenesExpressedHigherThanExpected-methods.Rd man/getNgenesFromMultiGroupStats-methods.Rd man/getSymbols-methods.Rd man/getTopSigGenes-methods.Rd man/group_intersect_order-methods.Rd man/groups_boxplot-methods.Rd man/heatPlotTimelines2D-methods.Rd man/human.CellSurface.Rd man/human.tfs.Rd man/loadObj-methods.Rd man/load_CellexalVR_selection-methods.Rd man/logThis-methods.Rd man/mds-methods.Rd man/merge-methods.Rd man/merge_cells-methods.Rd man/mouse.CellSurface.Rd man/mouse.tfs.Rd man/normalize.Rd man/normalize_R_buggy.Rd man/ontologyLogPage-methods.Rd man/plot2col_barplot-methods.Rd man/plotCodonUsage-methods.Rd man/plotLegend-methods.Rd man/plotMDS-methods.Rd man/plot_velocyto-methods.Rd man/positivesOnly-methods.Rd man/preprocess-methods.Rd man/pseudotimeTest-methods.Rd man/pseudotimeTest3D-methods.Rd man/pwd-methods.Rd man/quality_of_fit-methods.Rd man/readLoomFile-methods.Rd man/reduceTo-methods.Rd man/removeNeg-methods.Rd man/renew-methods.Rd man/reorder.genes-methods.Rd man/reorder.samples-methods.Rd man/reorder_grouping-methods.Rd man/reorder_on_wilcox_results-methods.Rd man/rfCluster_col.Rd man/rfCluster_row.Rd man/rmdLink-methods.Rd man/rownames-methods.Rd man/runStats_inThread-methods.Rd man/sampleCodonUsage-methods.Rd man/saveObj-methods.Rd man/show-methods.Rd man/simpleAnova-methods.Rd man/stat_table-methods.Rd man/tRF.typeHeatmap-methods.Rd man/tRNAMINT.Rd man/tRNA_stats-methods.Rd man/transpose-methods.Rd man/useInbuiltGOIlists-methods.Rd man/vioplot-methods.Rd man/z.score-methods.Rd scratchbord/PutNewCodeHere.R scratchbord/print.R tests/test-Rcpp.R tests/testthat.R tests/testthat/test-BioData_class.R tests/testthat/test-BioData_z.score.R tests/testthat/test-RFclust_slurm.R tests/testthat/test-RFclustering_local.R tests/testthat/test-Rcpp.R tests/testthat/test-SingleCells_class.R tests/testthat/test-Split4Geo.r tests/testthat/test-collapse.R tests/testthat/test-complexHeatmap.R tests/testthat/test-mds.R tests/testthat/test-merge.R tests/testthat/test-pseudotimeTest.R tests/testthat/test-tRNAMINT.z.score.R tests/testthat/test-tRNAMINT_class.R tests/testthat/test_BioData_class.R tests/testthat/test_BioData_z.score.R tests/testthat/test_RFclust_slurm.R tests/testthat/test_RFclustering.R tests/testthat/test_RFclustering_slurm.R tests/testthat/test_SingleCells_class.R tests/testthat/test_Split4Geo.r tests/testthat/test_collapse.R tests/testthat/test_complexHeatmap.R tests/testthat/test_mds.R tests/testthat/test_tRNAMINT.z.score.R tests/testthat/test_tRNAMINT_class.R tests/testthat/test_z.score.R vignettes/ExcludeRPsl_genes_from_data.Rmd vignettes/StandardAnalysis.R vignettes/StandardAnalysis.Rmd vignettes_not_OK/StandardAnalysis.Rmd