├── .Rbuildignore ├── .Rhistory ├── .gitignore ├── BingleSeq.Rproj ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── bulk_compDataTab.R ├── bulk_deDataTab.R ├── bulk_filterDataTab.R ├── bulk_footprintTab.R ├── bulk_goDataTab.R ├── bulk_loadDataTab.R ├── bulk_plotDataTab.R ├── sc_clustTab.R ├── sc_compTab.R ├── sc_deTab.R ├── sc_footprintTab.R ├── sc_goTab.R ├── sc_loadDataTab.R ├── sc_normTab.R ├── sc_qcTab.R ├── server.R ├── startApp.R └── ui.R ├── README.md ├── figures ├── Bulk.png ├── Bulk_format.jpg ├── batchCorrected.jpg ├── bulk_GOhist.jpg ├── bulk_GOquery.PNG ├── bulk_GOresults.PNG ├── bulk_GOtab.PNG ├── bulk_compRank.PNG ├── bulk_compVenn.PNG ├── bulk_deData.PNG ├── bulk_heatmap.PNG ├── bulk_loadData.PNG ├── bulk_qcData.PNG ├── bulk_visData.PNG ├── footprint.PNG ├── meta_format.jpg ├── sc.jpg ├── sc3tSNE.png ├── sc_clustElbow.PNG ├── sc_clustHeat.PNG ├── sc_clustMonocle.PNG ├── sc_clustSC3.PNG ├── sc_clustSeurat.PNG ├── sc_deFigs.PNG ├── sc_deTab.PNG ├── sc_format.jpg ├── sc_normData.PNG ├── sc_qcData.PNG └── sc_variancePlot.PNG ├── inst └── extdata │ ├── MockvsIFN.txt │ ├── hg19 │ ├── barcodes.tsv │ ├── genes.tsv │ └── matrix.mtx │ └── m_ifn.csv ├── man ├── barTable.Rd ├── batchComBat.Rd ├── batchHarman.Rd ├── bulk_compData.Rd ├── bulk_compDataUI.Rd ├── bulk_deData.Rd ├── bulk_deDataUI.Rd ├── bulk_faData.Rd ├── bulk_faDataUI.Rd ├── bulk_filterData.Rd ├── bulk_filterDataUI.Rd ├── bulk_goData.Rd ├── bulk_goDataUI.Rd ├── bulk_loadData.Rd ├── bulk_loadDataUI.Rd ├── bulk_plotData.Rd ├── bulk_plotDataUI.Rd ├── clusterMonocle.Rd ├── convert_gene_type.Rd ├── deEdgeR.Rd ├── deLimma.Rd ├── dePipelineCaller.Rd ├── deSequence.Rd ├── fetch_regulons.Rd ├── fetch_tf_activities.Rd ├── fetch_tfs_per_sample.Rd ├── filterFunction.Rd ├── genePlot.Rd ├── generateIntersect.Rd ├── generateSummary.Rd ├── getAllDE.Rd ├── getClusterHeatmap.Rd ├── getDEgenes.Rd ├── getGenesetsGO.Rd ├── getIntersect.Rd ├── get_pathway_activity.Rd ├── get_pathway_activity_per_sample.Rd ├── get_progeny_scatter.Rd ├── goInfo.Rd ├── histGoTerms.Rd ├── load10xData.Rd ├── normalizeSeurat.Rd ├── plotAllVenn.Rd ├── plotBarChart.Rd ├── plotHeatmapTop.Rd ├── plotMA.Rd ├── plotPCA.Rd ├── plotScree.Rd ├── plotVP.Rd ├── plot_tfa_per_sample.Rd ├── plot_top_tfs.Rd ├── qcHist.Rd ├── rankConsesus.Rd ├── runGOSEQ.Rd ├── sc3Cluster.Rd ├── sc_clust.Rd ├── sc_clustUI.Rd ├── sc_comp.Rd ├── sc_compUI.Rd ├── sc_de.Rd ├── sc_deUI.Rd ├── sc_dorothea_plot.Rd ├── sc_dorothea_viper.Rd ├── sc_faUI.Rd ├── sc_fa_Server.Rd ├── sc_getAllDE.Rd ├── sc_getDEgenes.Rd ├── sc_go.Rd ├── sc_goUI.Rd ├── sc_loadData.Rd ├── sc_loadDataUI.Rd ├── sc_norm.Rd ├── sc_normUI.Rd ├── sc_progeny.Rd ├── sc_progeny_plot.Rd ├── sc_qc.Rd ├── sc_qcUI.Rd ├── server.Rd ├── seuratElbow.Rd ├── seuratQC.Rd ├── startBingleSeq.Rd ├── sueratClust.Rd └── ui.Rd └── package_references.txt /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.Rhistory: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/.Rhistory -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/.gitignore -------------------------------------------------------------------------------- /BingleSeq.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/BingleSeq.Rproj -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/LICENSE -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/bulk_compDataTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/bulk_compDataTab.R -------------------------------------------------------------------------------- /R/bulk_deDataTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/bulk_deDataTab.R -------------------------------------------------------------------------------- /R/bulk_filterDataTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/bulk_filterDataTab.R -------------------------------------------------------------------------------- /R/bulk_footprintTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/bulk_footprintTab.R -------------------------------------------------------------------------------- /R/bulk_goDataTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/bulk_goDataTab.R -------------------------------------------------------------------------------- /R/bulk_loadDataTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/bulk_loadDataTab.R -------------------------------------------------------------------------------- /R/bulk_plotDataTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/bulk_plotDataTab.R -------------------------------------------------------------------------------- /R/sc_clustTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/sc_clustTab.R -------------------------------------------------------------------------------- /R/sc_compTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/sc_compTab.R -------------------------------------------------------------------------------- /R/sc_deTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/sc_deTab.R -------------------------------------------------------------------------------- /R/sc_footprintTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/sc_footprintTab.R -------------------------------------------------------------------------------- /R/sc_goTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/sc_goTab.R -------------------------------------------------------------------------------- /R/sc_loadDataTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/sc_loadDataTab.R -------------------------------------------------------------------------------- /R/sc_normTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/sc_normTab.R -------------------------------------------------------------------------------- /R/sc_qcTab.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/sc_qcTab.R -------------------------------------------------------------------------------- /R/server.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/server.R -------------------------------------------------------------------------------- /R/startApp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/startApp.R -------------------------------------------------------------------------------- /R/ui.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/R/ui.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/README.md -------------------------------------------------------------------------------- /figures/Bulk.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/Bulk.png -------------------------------------------------------------------------------- /figures/Bulk_format.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/Bulk_format.jpg -------------------------------------------------------------------------------- /figures/batchCorrected.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/batchCorrected.jpg -------------------------------------------------------------------------------- /figures/bulk_GOhist.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/bulk_GOhist.jpg -------------------------------------------------------------------------------- /figures/bulk_GOquery.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/bulk_GOquery.PNG -------------------------------------------------------------------------------- /figures/bulk_GOresults.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/bulk_GOresults.PNG -------------------------------------------------------------------------------- /figures/bulk_GOtab.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/bulk_GOtab.PNG -------------------------------------------------------------------------------- /figures/bulk_compRank.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/bulk_compRank.PNG -------------------------------------------------------------------------------- /figures/bulk_compVenn.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/bulk_compVenn.PNG -------------------------------------------------------------------------------- /figures/bulk_deData.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/bulk_deData.PNG -------------------------------------------------------------------------------- /figures/bulk_heatmap.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/bulk_heatmap.PNG -------------------------------------------------------------------------------- /figures/bulk_loadData.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/bulk_loadData.PNG -------------------------------------------------------------------------------- /figures/bulk_qcData.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/bulk_qcData.PNG -------------------------------------------------------------------------------- /figures/bulk_visData.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/bulk_visData.PNG -------------------------------------------------------------------------------- /figures/footprint.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/footprint.PNG -------------------------------------------------------------------------------- /figures/meta_format.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/meta_format.jpg -------------------------------------------------------------------------------- /figures/sc.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc.jpg -------------------------------------------------------------------------------- /figures/sc3tSNE.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc3tSNE.png -------------------------------------------------------------------------------- /figures/sc_clustElbow.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc_clustElbow.PNG -------------------------------------------------------------------------------- /figures/sc_clustHeat.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc_clustHeat.PNG -------------------------------------------------------------------------------- /figures/sc_clustMonocle.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc_clustMonocle.PNG -------------------------------------------------------------------------------- /figures/sc_clustSC3.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc_clustSC3.PNG -------------------------------------------------------------------------------- /figures/sc_clustSeurat.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc_clustSeurat.PNG -------------------------------------------------------------------------------- /figures/sc_deFigs.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc_deFigs.PNG -------------------------------------------------------------------------------- /figures/sc_deTab.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc_deTab.PNG -------------------------------------------------------------------------------- /figures/sc_format.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc_format.jpg -------------------------------------------------------------------------------- /figures/sc_normData.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc_normData.PNG -------------------------------------------------------------------------------- /figures/sc_qcData.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc_qcData.PNG -------------------------------------------------------------------------------- /figures/sc_variancePlot.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/figures/sc_variancePlot.PNG -------------------------------------------------------------------------------- /inst/extdata/MockvsIFN.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/inst/extdata/MockvsIFN.txt -------------------------------------------------------------------------------- /inst/extdata/hg19/barcodes.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/inst/extdata/hg19/barcodes.tsv -------------------------------------------------------------------------------- /inst/extdata/hg19/genes.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/inst/extdata/hg19/genes.tsv -------------------------------------------------------------------------------- /inst/extdata/hg19/matrix.mtx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/inst/extdata/hg19/matrix.mtx -------------------------------------------------------------------------------- /inst/extdata/m_ifn.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/inst/extdata/m_ifn.csv -------------------------------------------------------------------------------- /man/barTable.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/barTable.Rd -------------------------------------------------------------------------------- /man/batchComBat.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/batchComBat.Rd -------------------------------------------------------------------------------- /man/batchHarman.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/batchHarman.Rd -------------------------------------------------------------------------------- /man/bulk_compData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_compData.Rd -------------------------------------------------------------------------------- /man/bulk_compDataUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_compDataUI.Rd -------------------------------------------------------------------------------- /man/bulk_deData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_deData.Rd -------------------------------------------------------------------------------- /man/bulk_deDataUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_deDataUI.Rd -------------------------------------------------------------------------------- /man/bulk_faData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_faData.Rd -------------------------------------------------------------------------------- /man/bulk_faDataUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_faDataUI.Rd -------------------------------------------------------------------------------- /man/bulk_filterData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_filterData.Rd -------------------------------------------------------------------------------- /man/bulk_filterDataUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_filterDataUI.Rd -------------------------------------------------------------------------------- /man/bulk_goData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_goData.Rd -------------------------------------------------------------------------------- /man/bulk_goDataUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_goDataUI.Rd -------------------------------------------------------------------------------- /man/bulk_loadData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_loadData.Rd -------------------------------------------------------------------------------- /man/bulk_loadDataUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_loadDataUI.Rd -------------------------------------------------------------------------------- /man/bulk_plotData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_plotData.Rd -------------------------------------------------------------------------------- /man/bulk_plotDataUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/bulk_plotDataUI.Rd -------------------------------------------------------------------------------- /man/clusterMonocle.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/clusterMonocle.Rd -------------------------------------------------------------------------------- /man/convert_gene_type.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/convert_gene_type.Rd -------------------------------------------------------------------------------- /man/deEdgeR.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/deEdgeR.Rd -------------------------------------------------------------------------------- /man/deLimma.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/deLimma.Rd -------------------------------------------------------------------------------- /man/dePipelineCaller.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/dePipelineCaller.Rd -------------------------------------------------------------------------------- /man/deSequence.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/deSequence.Rd -------------------------------------------------------------------------------- /man/fetch_regulons.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/fetch_regulons.Rd -------------------------------------------------------------------------------- /man/fetch_tf_activities.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/fetch_tf_activities.Rd -------------------------------------------------------------------------------- /man/fetch_tfs_per_sample.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/fetch_tfs_per_sample.Rd -------------------------------------------------------------------------------- /man/filterFunction.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/filterFunction.Rd -------------------------------------------------------------------------------- /man/genePlot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/genePlot.Rd -------------------------------------------------------------------------------- /man/generateIntersect.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/generateIntersect.Rd -------------------------------------------------------------------------------- /man/generateSummary.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/generateSummary.Rd -------------------------------------------------------------------------------- /man/getAllDE.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/getAllDE.Rd -------------------------------------------------------------------------------- /man/getClusterHeatmap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/getClusterHeatmap.Rd -------------------------------------------------------------------------------- /man/getDEgenes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/getDEgenes.Rd -------------------------------------------------------------------------------- /man/getGenesetsGO.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/getGenesetsGO.Rd -------------------------------------------------------------------------------- /man/getIntersect.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/getIntersect.Rd -------------------------------------------------------------------------------- /man/get_pathway_activity.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/get_pathway_activity.Rd -------------------------------------------------------------------------------- /man/get_pathway_activity_per_sample.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/get_pathway_activity_per_sample.Rd -------------------------------------------------------------------------------- /man/get_progeny_scatter.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/get_progeny_scatter.Rd -------------------------------------------------------------------------------- /man/goInfo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/goInfo.Rd -------------------------------------------------------------------------------- /man/histGoTerms.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/histGoTerms.Rd -------------------------------------------------------------------------------- /man/load10xData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/load10xData.Rd -------------------------------------------------------------------------------- /man/normalizeSeurat.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/normalizeSeurat.Rd -------------------------------------------------------------------------------- /man/plotAllVenn.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/plotAllVenn.Rd -------------------------------------------------------------------------------- /man/plotBarChart.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/plotBarChart.Rd -------------------------------------------------------------------------------- /man/plotHeatmapTop.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/plotHeatmapTop.Rd -------------------------------------------------------------------------------- /man/plotMA.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/plotMA.Rd -------------------------------------------------------------------------------- /man/plotPCA.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/plotPCA.Rd -------------------------------------------------------------------------------- /man/plotScree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/plotScree.Rd -------------------------------------------------------------------------------- /man/plotVP.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/plotVP.Rd -------------------------------------------------------------------------------- /man/plot_tfa_per_sample.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/plot_tfa_per_sample.Rd -------------------------------------------------------------------------------- /man/plot_top_tfs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/plot_top_tfs.Rd -------------------------------------------------------------------------------- /man/qcHist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/qcHist.Rd -------------------------------------------------------------------------------- /man/rankConsesus.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/rankConsesus.Rd -------------------------------------------------------------------------------- /man/runGOSEQ.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/runGOSEQ.Rd -------------------------------------------------------------------------------- /man/sc3Cluster.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc3Cluster.Rd -------------------------------------------------------------------------------- /man/sc_clust.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_clust.Rd -------------------------------------------------------------------------------- /man/sc_clustUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_clustUI.Rd -------------------------------------------------------------------------------- /man/sc_comp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_comp.Rd -------------------------------------------------------------------------------- /man/sc_compUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_compUI.Rd -------------------------------------------------------------------------------- /man/sc_de.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_de.Rd -------------------------------------------------------------------------------- /man/sc_deUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_deUI.Rd -------------------------------------------------------------------------------- /man/sc_dorothea_plot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_dorothea_plot.Rd -------------------------------------------------------------------------------- /man/sc_dorothea_viper.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_dorothea_viper.Rd -------------------------------------------------------------------------------- /man/sc_faUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_faUI.Rd -------------------------------------------------------------------------------- /man/sc_fa_Server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_fa_Server.Rd -------------------------------------------------------------------------------- /man/sc_getAllDE.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_getAllDE.Rd -------------------------------------------------------------------------------- /man/sc_getDEgenes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_getDEgenes.Rd -------------------------------------------------------------------------------- /man/sc_go.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_go.Rd -------------------------------------------------------------------------------- /man/sc_goUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_goUI.Rd -------------------------------------------------------------------------------- /man/sc_loadData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_loadData.Rd -------------------------------------------------------------------------------- /man/sc_loadDataUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_loadDataUI.Rd -------------------------------------------------------------------------------- /man/sc_norm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_norm.Rd -------------------------------------------------------------------------------- /man/sc_normUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_normUI.Rd -------------------------------------------------------------------------------- /man/sc_progeny.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_progeny.Rd -------------------------------------------------------------------------------- /man/sc_progeny_plot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_progeny_plot.Rd -------------------------------------------------------------------------------- /man/sc_qc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_qc.Rd -------------------------------------------------------------------------------- /man/sc_qcUI.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sc_qcUI.Rd -------------------------------------------------------------------------------- /man/server.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/server.Rd -------------------------------------------------------------------------------- /man/seuratElbow.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/seuratElbow.Rd -------------------------------------------------------------------------------- /man/seuratQC.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/seuratQC.Rd -------------------------------------------------------------------------------- /man/startBingleSeq.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/startBingleSeq.Rd -------------------------------------------------------------------------------- /man/sueratClust.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/sueratClust.Rd -------------------------------------------------------------------------------- /man/ui.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/man/ui.Rd -------------------------------------------------------------------------------- /package_references.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dbdimitrov/BingleSeq/HEAD/package_references.txt --------------------------------------------------------------------------------