Man pages for FerrenaAlexander/FerrenaBulkRNAseq
Pipeline for analysis of bulkRNAseq data
| gsea.dotplot.onecol | Plot GSEA results as a dotplot |
| gsea.results | Get GSEA results |
| heatmapplot | Make an expression heatmap with hierarchical clustering |
| markerheatmap | Marker annotated heatmap |
| modulescore | Calculate a sample-wise module score given a list of genes |
| pathwayanalysis | Run Overrepresentation Analysis via the ClusterProfiler... |
| pathwayanalysis_declare_significant_clusters | Declare significant clusters in the output of pathway... |
| pathwayanalysis_finalize_emap_plots | Add more emapplots (graph plots with edges between similar... |
| pathwayanalysis_relabel_significant_clusters | Relabel some pathway clusters with biologically relevant... |
| pathwayanalysis_sigcluster_subplots | Make plots for pathways in each cluster. |
| pathwayanalysis_venn | Make a Venn Diagram with genes from the significant clusters. |
| pathwayanalysis_wordcloud | A fast way to make a wordcloud from a character vector of... |
| regressout | Regress out a variable from a gene expression matrix with... |
| survival | A function for survival analysis. |
| volcanoplot | Make a VolcanoPlot |
