Man pages for calebclass/NanoTube
An Easy Pipeline for NanoString nCounter Data Analysis
| deVolcano | Draw volcano plot of differential expression results |
| ExamplePathways | Example pathway database |
| ExampleResults | Example results from runLimmaAnalysis |
| fgseaPostprocessing | Postprocessing for GSEA analyses |
| fgseaPostprocessingXLSX | Postprocessing for GSEA analyses for Excel |
| fgseaToLEdge | Generate leading edge matrix from fgsea results. |
| gm_mean | Calculate the geometric mean |
| groupedGSEAtoStackedReport | Build a report from gene set enrichment results. |
| groupFGSEA | Cluster gene set analysis results |
| limmaToFGSEA | Run gene set enrichment analysis using DE results. |
| makeDiffExprFile | Make differential expression results file. |
| makeFGSEAmasterTable | Make master table of all GSEA results |
| makeNanoStringSetFromEset | Convert NanoString ExpressionSet to NanoStringSet |
| nanostringPCA | Plot PCA |
| NanoTube | NanoTube |
| negativeQC | Calculate negative control statistics |
| normalize_housekeeping | Housekeeping gene normalization |
| normalize_pos_controls | Positive control gene normalization |
| nsdiffToFGSEA | Run gene set enrichment analysis using DE results. |
| positiveQC | Calculate positive control statistics |
| processNanostringData | Process NanoString nCounter gene expression data. |
| read_cpdb_sourceDBs | Identify source databases from a .tab file |
| read_cpdb_tab | Read .tab file. |
| read_merge_rcc | Merge multiple .rcc files |
| read_rcc | Read .rcc file |
| read_sampleData | Read in a sample data table. |
| remove_background | Assess background expression |
| runLimmaAnalysis | Conduct differential expression analysis |
| untar_dirs | Untar |
| unzip_dirs | Unzip |
