Files in barzine/barzinePhdR

Code developed while and for my PhD thesis at the EMBL-EBI

R/barzinePhdR-package.R R/data-prep.R R/data.R R/descriptors.R R/fromGplots.R R/geneClassifications.R R/genes-meta-analyses.R R/ggplot-extras.R R/go-related.R R/graphics.R R/heatmap-wrappers.R R/internals.R R/io.R R/metaAnalyses.R R/misc-deprecated.R R/misc-helpers.R R/report-helpers.R R/scatter-plots.R R/selection-filtering.R R/utils-DF.R R/utils-genesExpDF.R R/utils.R R/vennDiag.R R/zzz.R README.md man/Cumulative_spe.Rd man/DrawVenn.Rd man/ExpressedGeneInTissue.Rd man/Intersect.Rd man/List.Rd man/ListOfExpressedGenes.Rd man/Load.Rd man/NAto0.Rd man/Read.table.Rd man/RowMad.Rd man/RowMeans.Rd man/RowMedians.Rd man/RowMode.Rd man/Union.Rd man/add.qual.att.Rd man/barplotCommonGenesUnique2D.Rd man/barplotCommonGenesUnique3D.Rd man/bibarplotsDiversityCond.Rd man/bluered.Rd man/boolDF2numeric.Rd man/cat.html.Rd man/change.localID.Rd man/checkConformity.Rd man/clean.HTSc.Rd man/clean.infinite.Rd man/cleanNames.Rd man/cleanReadAnnot.Rd man/cleantable.Rd man/colCbc.Rd man/colMax.Rd man/colMin.Rd man/colSelect.Rd man/colSelect2.Rd man/colorpanel.Rd man/comp_cor_log2.Rd man/comp_ratio_sd.Rd man/complement2nbGenesPerCond.unique.Rd man/completeDF.t_test.CorrMat_identical.vs.different.Rd man/computeBreadth.Rd man/compute_gene_cor.Rd man/compute_gene_cor_save.Rd man/compute_permuted_cor.Rd man/compute_permuted_corQ.Rd man/compute_tissue_corr_matrix.Rd man/createDFhXg.Rd man/createGoAnnot.Rd man/createTableResults_basics.Rd man/creationDf.gxa.Rd man/cross.select.Rd man/cross.selectCond.Rd man/cross.sharedDistrib.Rd man/cross.sharedDistrib_firstLast.Rd man/crudeStrip.Rd man/cumulSpe.Rd man/cumulSpeSimulAggregated.Rd man/cutoff.Rd man/dataset.HTSc.Rd man/dataset.randomize.Rd man/dataset_irap.Rd man/datatable.custom.Rd man/density_plot.Rd man/df.Strip.Rd man/df.StripLine.Rd man/df.cutoff.Rd man/df.cutoff2.Rd man/df.fill.Rd man/drawOverlapHeatmaps.Rd man/ebiRank.Rd man/enhancedTissue.Rd man/enrichedTissue.Rd man/evolCorrCumul.Rd man/evolCvCorrCumul.Rd man/excludeGenes.Rd man/excludeRows.Rd man/extract.HTSc.Rd man/extract.irap.Rd man/extractDendroFromPlotTD.Rd man/extractDendroTissueDistance.Rd man/extractSpe.Rd man/extractWithTag.Rd man/extractWithinSampleAbundance.Rd man/extractWithinSampleTop3Abundance.Rd man/factorDF2string.Rd man/factoring.Rd man/factoring.rbind.Rd man/filtre.dataset.Rd man/fixNamesGtex.Rd man/fixNamesUhlen.Rd man/g_legend.Rd man/gen.add.qual.att.Rd man/geneClassify.Q.Rd man/geneClassify.Rd man/geneScatters.Rd man/getEpsilon.Rd man/gg_color_hue.Rd man/go2genes.Rd man/grapes-greater-than-equals-grapes.Rd man/grapes-less-than-equals-grapes.Rd man/greenred.Rd man/hampel.test.Rd man/heatmap.2.Rd man/heatmapAlpabet.Rd man/heatmapAlphabet.Rd man/heatmapWithClustering.Rd man/initialise.Rd man/internalJaccardIndMatrix.Rd man/jaccardInd.Rd man/lg.format.Rd man/listFromFile.Rd man/listFromFileBiomart.Rd man/listgenes.Rd man/load_and_check_3DF.Rd man/log2.na.Rd man/mHeatmap.Rd man/mHeatmapTC.Rd man/make.2ldf.Rd man/make.3ldf.Rd man/matchColCond.Rd man/matrix.overlap_res.Rd man/maxCond.df.Rd man/merge_biol_rep.Rd man/merge_replicates.Rd man/merge_tech_rep.Rd man/mixed.high.Rd man/mixed.high2.Rd man/mixed.low.Rd man/mixed.low2.Rd man/mkMatrix.Rd man/multi.add.qual.att.Rd man/multibarplotsDiversityCond.Rd man/nameID.Rd man/nbGenesPerCond.Rd man/nbGenesPerCond.unique.Rd man/nl1d.Rd man/noMoreFactor.Rd man/overlapProtTrans.Specific.Rd man/overlapSortCumul2DF.Rd man/overlapSortCumul5DF.Rd man/overlapSpeProtmRNA.Rd man/plotGOHeatmap.Rd man/plotTissuesDistance.Rd man/plotUniq.distrib.Rd man/plot_distribDF.Rd man/plot_xsharedDistrib.Rd man/prefix.Rd man/prefixv.Rd man/presentData.Rd man/printDebug.Rd man/protSpe.Rd man/qLoad.Rd man/rank.Atlas.Rd man/rankSpe.Rd man/ratioSpe.1.Rd man/ratioSpe.Rd man/read.list.Rd man/redblue.Rd man/redgreen.Rd man/refGraphDF.Rd man/relative.GXenrichement.Rd man/relative.GXenrichement2.Rd man/relnum.GXenrichement.Rd man/removeClusters.Rd man/replotCumulSpeSimulAggregated.Rd man/revCustom.Rd man/revCustomMatrixDist.Rd man/rowCV.Rd man/rowMax.Rd man/rowMin.Rd man/rowSD.Rd man/rowVar.Rd man/rpkm2tpm.Rd man/saveToFile.Rd man/saveWithName.Rd man/save_df.Rd man/scatplot.Rd man/scatplot.log2.Rd man/selectSpecific.Rd man/setDebug.Rd man/setEpsilon.Rd man/sharedBreadth.Rd man/signifDF.Rd man/simpleCap.Rd man/simpleCap2.Rd man/single.factoring.Rd man/single.factoring2.Rd man/sortUhlenClassInOne.Rd man/sortedGenesCorr.Rd man/stamped.Rd man/stat.mode.Rd man/strip.Rd man/subset-.result.Rd man/substrRight.Rd man/suffix.Rd man/t_test.CorrMat_identical.vs.different.Rd man/t_test.Mat_identical.vs.different.Rd man/tableGeneIDdesc.Rd man/test_CorrMat_identical_different.Rd man/theme_cbw.Rd man/theme_legacy.Rd man/theme_minimaliste.Rd man/tissuesDistance.Rd man/topCommonGenes.Rd man/topgenes.corCluster.Rd man/topgenes.corClusterDraw.Rd man/topgenes.corClusterDraw_log.Rd man/topgenes.corCluster_log.Rd man/trimSpace.Rd man/ubi.high.Rd man/ubi.low.Rd man/ubi.strict.Rd man/undetected.Rd man/unmatchedRowsAbyB.Rd man/unmatchedRowsAbyBC.Rd man/usablePath.Rd man/vennPlot_spe.Rd man/wrap.compute_permuted_corQ_save.Rd man/wrap.scatplot.log2.Rd man/wtDF.Rd man/xsharedDistrib.Rd vignettes/Startpoint.Rmd