# An Easy Pipeline for NanoString nCounter Data Analysis

## Documentation for package ‘NanoTube’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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