An Easy Pipeline for NanoString nCounter Data Analysis

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Documentation for package ‘NanoTube’ version 1.4.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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