Files in stela2502/StefansExpressionSet

StefansExpressionSet

R/011_class_func.R R/01_class.R R/02_collaps.R R/02_drop.samples.R R/02_loadObj.R R/02_reduce.Obj.R R/02_reorder.obj.R R/02_restrictSamples.R R/02_saveObj.R R/02_set.outpath.R R/02_transpose.R R/03_check.depth.R R/03_ranks.R R/03_reads.taken.R R/EXTERNAL_heatmap.3.R R/Grouoing.qualityTest.R R/Grouping.addCluster.R R/Grouping.bestGrouping.R R/Grouping.difference.R R/Grouping.hclust.R R/Grouping.identifyBestGrouping.R R/Grouping.predict.rf.R R/Grouping.quality_of_fit.R R/Grouping.rfCluster_col.R R/Grouping.rfCluster_row.R R/Groups.color_4.R R/MDS.Make3D4Obj.R R/MDS.clusters.R R/MDS.mds.R R/add2usedObj.R R/addAnnotation.R R/anayse_working_set.R R/as.BioData.R R/as.NGSexpressionSet.R R/describe.probeset.R R/getAnnotation4probesets.R R/getProbesetsFromStats.R R/getProbesetsFromValues.R R/get_gene_list.R R/interesting_genes.R R/log2.R R/name_4_IDs.R R/plot.complexHeatmap.R R/plot.gg.defineHeatmapColors.R R/plot.gg.heatmap.list.R R/plot.gg.melt.StefansExpressionSet.R R/plot.gg.melt.addGeneColGroup.R R/plot.gg.melt.addSampleColGroup.R R/plot.ggplot.gene.R R/plot.groups.boxplot.R R/plot.heatmaps.R R/plot.histogram.R R/plot.legend.R R/plot.probeset.R R/plot.stats.as.heatmap.R R/read.bams.R R/removeBatch.R R/show.R R/stat.coexprees4gene.R R/stat.corMat.R R/stat.createStats.R R/stat.normalize.R R/stat.pcorMat.R R/stat.preprocess.R R/stat.simpleAnova.R R/stat.z.score.R R/stat_sd.filter.R R/update.measurements.R R/write.4GEDI.R R/write.cor2cytoscape.R R/write.data.R R/write.export.data.R R/writeStatTables.R R/x_force.numeric.R R/x_forceAbsoluteUniqueSample.R R/x_pwd.R Readme.md install.R man/FromCountsObj-methods.Rd man/Make3D4obj-methods.Rd man/NGSexpressionSet-methods.Rd man/NGSexpressionSet.Rd man/PMID25158935exp.Rd man/PMID25158935samples.Rd man/SingleCellsNGS-methods.Rd man/SingleCellsNGS.Rd man/StefansExpressionSet-methods.Rd man/StefansExpressionSet.Rd man/add2usedObj-methods.Rd man/addAnnotation-methods.Rd man/addCluster-methods.Rd man/addGeneColGroup-methods.Rd man/addSampleColGroup-methods.Rd man/anayse_working_set-methods.Rd man/as_BioData-methods.Rd man/as_NGSexpressionSet-methods.Rd man/bestGrouping.Rd man/check.depth-methods.Rd man/clusters-methods.Rd man/coexprees4gene-methods.Rd man/collaps-methods.Rd man/colors_4-methods.Rd man/complexHeatmap-methods.Rd man/cor2cytoscape-methods.Rd man/corMat-methods.Rd man/createRFgrouping_col-methods.Rd man/createRFgrouping_row-methods.Rd man/createStats-methods.Rd man/defineHeatmapColors-methods.Rd man/describe.probeset-methods.Rd man/difference-methods.Rd man/drop.samples-methods.Rd man/export.data-methods.Rd man/export4GEDI-methods.Rd man/force.numeric-methods.Rd man/forceAbsoluteUniqueSample-methods.Rd man/getAnnotation4probesets-methods.Rd man/getProbesetsFromStats-methods.Rd man/getProbesetsFromValues-methods.Rd man/get_gene_list-methods.Rd man/gg.heatmap.list-methods.Rd man/ggplot.gene-methods.Rd man/group.hclust-methods.Rd man/groups.boxplot-methods.Rd man/identifyBestGrouping-methods.Rd man/interesting_genes-methods.Rd man/loadObj-methods.Rd man/log2-methods.Rd man/mds-methods.Rd man/melt-methods.Rd man/minValueExpr-methods.Rd man/name_4_IDs-methods.Rd man/normalize-methods.Rd man/pcorMat-methods.Rd man/plot-methods.Rd man/plot.heatmaps-methods.Rd man/plot.legend-methods.Rd man/plot.probeset-methods.Rd man/plot_histogram-methods.Rd man/predict.rf.Rd man/preprocess-methods.Rd man/pwd-methods.Rd man/qualityTest-methods.Rd man/quality_of_fit-methods.Rd man/ranks-methods.Rd man/read.bams-methods.Rd man/reads.taken-methods.Rd man/red.Rd man/reduce.Obj-methods.Rd man/removeBatch-methods.Rd man/reorder.genes-methods.Rd man/reorder.samples-methods.Rd man/restrictSamples-methods.Rd man/rfCluster_col.Rd man/rfCluster_row.Rd man/saveObj-methods.Rd man/sd.filter-methods.Rd man/set.outpath-methods.Rd man/show-methods.Rd man/simpleAnova-methods.Rd man/transpose-methods.Rd man/update.measurements-methods.Rd man/write.data-methods.Rd man/writeStatTables-methods.Rd man/z.score-methods.Rd oldR/Accessors.R oldR/Clusters.R oldR/StefansExpressionSet.R tests/testthat.R tests/testthat/test.ExpressionSet.r unusedR/ArrayExpressionSet.R unusedR/ExpressionSet.R unusedR/ExpressionSet_Cluster.R unusedR/PathwaysGMT.R unusedR/RFgrouping.R unusedR/Tool_RandomForest.R unusedR/ggplot_heatmap_fesability_study.R vignettes/NGSexpressionSet.pdf