Files in chrarnold/GRaNIE

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

NEWS.md R/DataClasses.R R/GRN.R R/core.R R/diffTF_sharedFunctions.R R/helperFunctions.R R/network.R R/plot.R R/zzz.R README.md man-roxygen/GRN.R man-roxygen/TF_peak.connectionTypes.R man-roxygen/addRobustRegression.R man-roxygen/basenameOutput.R man-roxygen/corMethod.R man-roxygen/forceRerun.R man-roxygen/gene.types.R man-roxygen/nCores.R man-roxygen/name_TFActivity.R man-roxygen/normalization.R man-roxygen/normalization_TFActivity.R man-roxygen/outputFolder.R man-roxygen/pages.R man-roxygen/pdf_height.R man-roxygen/pdf_width.R man-roxygen/permutation.R man-roxygen/permuted.R man-roxygen/plotAsPDF.R man-roxygen/plotDetails.R man-roxygen/plotDiagnosticPlots.R man/AR_classification_wrapper.Rd man/GRN-class.Rd man/GRaNIE.Rd man/addConnections_TF_peak.Rd man/addConnections_peak_gene.Rd man/addData.Rd man/addData_TFActivity.Rd man/addTFBS.Rd man/add_TF_gene_correlation.Rd man/build_eGRN_graph.Rd man/calculateCommunitiesEnrichment.Rd man/calculateCommunitiesStats.Rd man/calculateGeneralEnrichment.Rd man/calculateTFEnrichment.Rd man/changeOutputDirectory.Rd man/deleteIntermediateData.Rd man/filterData.Rd man/filterGRNAndConnectGenes.Rd man/generateStatsSummary.Rd man/genes-methods.Rd man/getCounts.Rd man/getGRNConnections.Rd man/getParameters.Rd man/getTopNodes.Rd man/importTFData.Rd man/initializeGRN.Rd man/loadExampleObject.Rd man/overlapPeaksAndTFBS.Rd man/peaks-methods.Rd man/performAllNetworkAnalyses.Rd man/plotCommunitiesEnrichment.Rd man/plotCommunitiesStats.Rd man/plotDiagnosticPlots_TFPeaks.Rd man/plotDiagnosticPlots_peakGene.Rd man/plotGeneralEnrichment.Rd man/plotGeneralGraphStats.Rd man/plotPCA_all.Rd man/plotTFEnrichment.Rd man/plot_stats_connectionSummary.Rd man/visualizeGRN.Rd tests/testthat.R tests/testthat/test-first_test.R vignettes/GRaNIE_workflow.Rmd