Package: NanoTube 1.19.0

Caleb Class

NanoTube: An Easy Pipeline for NanoString nCounter Data Analysis

NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages.

Authors:Caleb Class [cre, aut], Caiden Lukan [ctb]

NanoTube_1.19.0.tar.gz
NanoTube_1.19.0.zip(r-4.7)NanoTube_1.19.0.zip(r-4.6)NanoTube_1.19.0.zip(r-4.5)
NanoTube_1.19.0.tgz(r-4.6-any)NanoTube_1.19.0.tgz(r-4.5-any)
NanoTube_1.19.0.tar.gz(r-4.7-any)NanoTube_1.19.0.tar.gz(r-4.6-any)
NanoTube_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
NanoTube/json (API)

# Install 'NanoTube' in R:

install.packages('NanoTube', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

ExamplePathways - Example pathway database
ExampleResults - Example results from runLimmaAnalysis

On BioConductor:NanoTube-1.19.0(bioc 3.24)NanoTube-1.18.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software geneexpression differentialexpression qualitycontrol

4.00 score 9 scripts 26 exports 39 dependencies

Last updated from:cf02f2e565. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	188
linux-devel-x86_64	NOTE	255
source / vignettes	OK	273
linux-release-x86_64	NOTE	280
macos-release-arm64	NOTE	114
macos-oldrel-arm64	NOTE	125
windows-devel	NOTE	254
windows-release	NOTE	219
windows-oldrel	NOTE	204
wasm-release	OK	200

Exports:deVolcano fgseaPostprocessing fgseaPostprocessingXLSX fgseaToLEdge gm_mean groupedGSEAtoStackedReport groupFGSEA limmaToFGSEA makeDiffExprFile makeNanoStringSetFromEset nanostringPCA negativeQC normalize_housekeeping normalize_pos_controls nsdiffToFGSEA positiveQC processNanostringData read_cpdb_sourceDBs read_cpdb_tab read_merge_rcc read_rcc read_sampleData remove_background runLimmaAnalysis untar_dirs unzip_dirs

Dependencies:BH Biobase BiocGenerics BiocParallel cli codetools cowplot cpp11 data.table farver fastmatch fgsea formatR futile.logger futile.options generics ggplot2 glue gtable isoband labeling lambda.r lattice lifecycle limma Matrix plyr R6 RColorBrewer Rcpp reshape rlang S7 scales snow statmod vctrs viridisLite withr

Analyzing NanoString nCounter Data with the NanoTube

Rendered fromNanoTube.Rmdusingknitr::rmarkdown

Last update: 2023-03-08
Started: 2020-09-29

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

Package: NanoTube 1.19.0

NanoTube: An Easy Pipeline for NanoString nCounter Data Analysis

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