Files in chrarnold/GRaNIE
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
.gitignore
DESCRIPTION
NAMESPACE
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
vignettes/custom.css
