├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R ├── DEfuns.R ├── DEpanel.R ├── DEplotFuns.R ├── DEplotPanel.R ├── DEsummaryFuns.R ├── DEsummaryPanel.R ├── GRNCisPanel.R ├── GRNCustomPanel.R ├── GRNTransPanel.R ├── GRNfuns.R ├── GRNpanel.R ├── QCpanel.R ├── QCplotFuns.R ├── crossPanel.R ├── cross_plot.R ├── enrichmentPanel.R ├── generateShinyApp.R ├── landingPanel.R ├── modalityPanel.R ├── patternFuns.R ├── patternPanel.R ├── preprocessExpressionMatrix.R ├── preprocess_miRTarBase.R ├── sampleSelectPanel.R └── utils-pipe.R ├── README.md ├── _pkgdown.yml ├── bulkAnalyseR.Rproj ├── docs ├── 404.html ├── LICENSE.html ├── articles │ ├── GEO_App.html │ ├── GEO_App_files │ │ └── figure-html │ │ │ └── preprocess-1.png │ ├── IntegratingMultiomics.html │ ├── bulkAnalyseR.html │ ├── bulkAnalyseR_files │ │ └── figure-html │ │ │ └── preprocess-1.png │ ├── figures │ │ ├── CisIntegrationExample.png │ │ ├── CrossPlot.png │ │ ├── CustomIntegrationExample.png │ │ ├── DE.png │ │ ├── Enrichment.png │ │ ├── EnrichmentIntegrationExample.png │ │ ├── ExpressionHeatmap.png │ │ ├── ExpressionPatterns.png │ │ ├── ExpressionPatternsHeatmap.png │ │ ├── ExpressionPatternsLinePlot.png │ │ ├── GRN.png │ │ ├── JSI.png │ │ ├── MAPlot.png │ │ ├── MA_QC.png │ │ ├── PCA.png │ │ ├── PCA_DE.png │ │ ├── SampleSelect.png │ │ ├── ScreenShot.png │ │ ├── TransIntegrationExample.png │ │ ├── VolcanoPlot.png │ │ └── workflow.png │ └── index.html ├── authors.html ├── code-color-scheme-dark.css ├── code-color-scheme-light.css ├── darkswitch.js ├── deps │ ├── bootstrap-5.1.0 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-5.1.3 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── data-deps.txt │ └── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map ├── figures │ └── bulkAnalyseR_Slides.pdf ├── index.html ├── link.svg ├── pkgdown.js ├── pkgdown.yml ├── preferably.css ├── reference │ ├── DEanalysis.html │ ├── DEpanel.html │ ├── DEplotPanel.html │ ├── DEsummaryPanel.html │ ├── GRNCisPanel.html │ ├── GRNCustomPanel.html │ ├── GRNTransPanel.html │ ├── GRNpanel.html │ ├── QCpanel.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── calculate_condition_mean_sd_per_gene.html │ ├── crossPanel.html │ ├── cross_plot-1.png │ ├── cross_plot.html │ ├── determine_uds.html │ ├── enrichmentPanel.html │ ├── expression_heatmap-1.png │ ├── expression_heatmap.html │ ├── find_regulators_with_recurring_edges.html │ ├── generateShinyApp.html │ ├── get_link_list_rename.html │ ├── index.html │ ├── infer_GRN.html │ ├── jaccard_heatmap-1.png │ ├── jaccard_heatmap.html │ ├── jaccard_index.html │ ├── landingPanel.html │ ├── libs │ │ ├── htmlwidgets-1.5.4 │ │ │ └── htmlwidgets.js │ │ ├── vis-9.1.0 │ │ │ ├── add_css.txt │ │ │ ├── img │ │ │ │ └── network │ │ │ │ │ ├── acceptDeleteIcon.png │ │ │ │ │ ├── addNodeIcon.png │ │ │ │ │ ├── backIcon.png │ │ │ │ │ ├── connectIcon.png │ │ │ │ │ ├── cross.png │ │ │ │ │ ├── cross2.png │ │ │ │ │ ├── deleteIcon.png │ │ │ │ │ ├── downArrow.png │ │ │ │ │ ├── editIcon.png │ │ │ │ │ ├── leftArrow.png │ │ │ │ │ ├── minus.png │ │ │ │ │ ├── plus.png │ │ │ │ │ ├── rightArrow.png │ │ │ │ │ ├── upArrow.png │ │ │ │ │ └── zoomExtends.png │ │ │ ├── vis-network.min.css │ │ │ └── vis-network.min.js │ │ └── visNetwork-binding-2.1.0 │ │ │ └── visNetwork.js │ ├── ma_plot-1.png │ ├── ma_plot.html │ ├── make_heatmap_matrix.html │ ├── make_pattern_matrix.html │ ├── modalityPanel.html │ ├── noisyr_counts_with_plot-1.png │ ├── noisyr_counts_with_plot.html │ ├── patternPanel.html │ ├── pipe.html │ ├── plot_GRN.html │ ├── plot_line_pattern-1.png │ ├── plot_line_pattern.html │ ├── plot_pca-1.png │ ├── plot_pca.html │ ├── plot_upset-1.png │ ├── plot_upset.html │ ├── preprocessExpressionMatrix-1.png │ ├── preprocessExpressionMatrix.html │ ├── preprocess_miRTarBase.html │ ├── rescale_matrix.html │ ├── sampleSelectPanel.html │ ├── volcano_plot-1.png │ └── volcano_plot.html ├── search.json └── sitemap.xml ├── exampledata ├── Li2021_miRNA_mRNA │ ├── expression_matrix_mRNA.csv │ ├── expression_matrix_mRNA_preprocessed.csv │ ├── expression_matrix_miRNA.csv │ └── expression_matrix_miRNA_preprocessed.csv └── Yang2019_ChIP │ ├── ChIP_expression_matrix_preprocessed.csv │ ├── ChIP_peak_coords.csv │ └── gene_coords_GRCm38.p6.csv ├── inst └── extdata │ ├── expression_matrix.csv │ ├── expression_matrix_preprocessed.csv │ └── mmu_MTI_sub.xls ├── man ├── DEanalysis.Rd ├── DEpanel.Rd ├── DEplotPanel.Rd ├── DEsummaryPanel.Rd ├── GRNCisPanel.Rd ├── GRNCustomPanel.Rd ├── GRNTransPanel.Rd ├── GRNpanel.Rd ├── QCpanel.Rd ├── calculate_condition_mean_sd_per_gene.Rd ├── crossPanel.Rd ├── cross_plot.Rd ├── determine_uds.Rd ├── enrichmentPanel.Rd ├── expression_heatmap.Rd ├── find_regulators_with_recurring_edges.Rd ├── generateShinyApp.Rd ├── genes_barplot.Rd ├── get_link_list_rename.Rd ├── infer_GRN.Rd ├── jaccard_heatmap.Rd ├── jaccard_index.Rd ├── landingPanel.Rd ├── ma_plot.Rd ├── make_heatmap_matrix.Rd ├── make_pattern_matrix.Rd ├── modalityPanel.Rd ├── noisyr_counts_with_plot.Rd ├── patternPanel.Rd ├── pipe.Rd ├── plot_GRN.Rd ├── plot_line_pattern.Rd ├── plot_pca.Rd ├── plot_upset.Rd ├── preprocessExpressionMatrix.Rd ├── preprocess_miRTarBase.Rd ├── qc_density_plot.Rd ├── qc_violin_plot.Rd ├── rescale_matrix.Rd ├── sampleSelectPanel.Rd ├── scatter_plot.Rd └── volcano_plot.Rd ├── tests ├── testthat.R └── testthat │ └── test-GRNfuns.R └── vignettes ├── GEO_App.R ├── GEO_App.Rmd ├── GEO_App.html ├── IntegratingMultiomics.R ├── IntegratingMultiomics.Rmd ├── IntegratingMultiomics.html ├── bulkAnalyseR.R ├── bulkAnalyseR.Rmd ├── bulkAnalyseR.html └── figures ├── CisIntegrationExample.png ├── CrossPlot.png ├── CustomIntegrationExample.png ├── DE.png ├── Enrichment.png ├── EnrichmentIntegrationExample.png ├── ExpressionHeatmap.png ├── ExpressionPatterns.png ├── ExpressionPatternsHeatmap.png 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