Man pages for dbdimitrov/BugleSeq
BingleSeq RNA-Seq Data Analysis
| barTable | Generate the corresponding table of the Barchart |
| batchComBat | ComBat Batch Effect Correction |
| batchHarman | Harman Batch Effect Correction |
| bulk_compData | Bulk Compare Data Server |
| bulk_compDataUI | Bulk Compare Data UI |
| bulk_deData | Differential Expression Tab Server |
| bulk_deDataUI | Differential Expression Tab UI |
| bulk_faData | Bulk FootPrint Tab Server |
| bulk_faDataUI | Bulk Functional Annotation Tab UI |
| bulk_filterData | Bulk Filter Tab Server |
| bulk_filterDataUI | Bulk Filter Tab UI |
| bulk_goData | Bulk Gene Ontology Tab Server |
| bulk_goDataUI | Bulk Functional Annotation Tab UI |
| bulk_loadData | Bulk load Data SERVER |
| bulk_loadDataUI | Bulk load Data UI |
| bulk_plotData | Bulk Plot Data Tab Server |
| bulk_plotDataUI | Bulk Plot Data UI |
| clusterMonocle | Monocle Clustering Pipeline |
| convert_gene_type | Gene type converter function |
| deEdgeR | EdgeR Differential Expression Pipeline |
| deLimma | Limma Differential Expression Pipeline |
| dePipelineCaller | Differential Expression Pipeline Caller |
| deSequence | DESeq2 Differential Expression Pipeline |
| fetch_regulons | Fetch Dorothea Regulon |
| fetch_tf_activities | Transcription Factor activity with DoRothEA |
| fetch_tfs_per_sample | TF activity per sample Sample DoRothEA |
| filterFunction | Filter Function |
| genePlot | Gene Plots across clusters |
| generateIntersect | Extract Intersects |
| generateSummary | Generate Summary |
| getAllDE | Bulk Generate Data required to compare DE Package Results |
| getClusterHeatmap | Cluster Heatmap |
| getDEgenes | Get Differentially Expressed Genes (Bulk) |
| getGenesetsGO | Get GO gene sets for GOSeq |
| getIntersect | Returns the Genes of a given intersect within the Venn... |
| get_pathway_activity | Fetch Pathway Activity |
| get_pathway_activity_per_sample | Fetch Pathway Activity per Sample |
| get_progeny_scatter | Fetch Progeny Scatter with top Genes |
| goInfo | Generate GO Term Info |
| histGoTerms | Generate GO Histogram |
| load10xData | Load 10x Data with TryCatch |
| normalizeSeurat | Single Cell Normalize function |
| plotAllVenn | Generate a Venn Diagram with DE genes |
| plotBarChart | Generate the Barchart |
| plotHeatmapTop | Generate a Heatmap |
| plotMA | Generate an MA plot |
| plotPCA | Plot PCA |
| plotScree | Plot Scree |
| plot_tfa_per_sample | Plot the top n TF activities per Sample in a heatmap |
| plot_top_tfs | Plot the top n NES for the TFs |
| plotVP | Generate a Volcano plot |
| qcHist | QC Histogram Function |
| rankConsesus | Generates a ranking consesus from the selected methods |
| runGOSEQ | Functional Annotation Pipeline (Both pipelines) |
| sc3Cluster | SC3 Clustering Pipeline |
| sc_clust | Single Cell Cluster Tab Server |
| sc_clustUI | Single Cell Cluster Tab UI |
| sc_comp | SC Compare Data Server |
| sc_compUI | Single Cell Compare Data UI |
| sc_de | Single Cell Differential Expession Tab Server |
| sc_deUI | Single Cell Differential Expession Tab UI |
| sc_dorothea_plot | Dorothea-Viper TF Activity Plot |
| sc_dorothea_viper | Dorothea-Viper TF Activity estimation |
| sc_fa_Server | Single cell FootPrint Tab Server |
| sc_faUI | Bulk Functional Annotation Tab UI |
| sc_getAllDE | SC Generate Data required to compare DE Method Results |
| sc_getDEgenes | Get Differentially Expressed Genes (Single Cell) |
| sc_go | SC Functional Annotation Tab Server |
| sc_goUI | SC Functional Annotation Tab UI |
| sc_loadData | Single Cell Load Data Server |
| sc_loadDataUI | Single Cell Load Data UI |
| sc_norm | Single Cell Normalize Tab Server |
| sc_normUI | Single Cell Normalize Tab UI |
| sc_progeny | Progeny Pathway Activity estimation |
| sc_progeny_plot | Progeny Pathway Activity Heatmap |
| sc_qc | Single Cell Quality Control UI |
| sc_qcUI | Single Cell Quality Control UI |
| server | Initialize Server |
| seuratElbow | Single Cell Scale and Dimension Reduction function |
| seuratQC | Single Cell Quality Control |
| startBingleSeq | Launch the application |
| sueratClust | Seurat Clustering Pipeline |
| ui | Initiate GUI |
