NanoTube
Bioc currentAn Easy Pipeline for NanoString nCounter Data Analysis
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
27 26 exported
Complexity
5.8 avg / 31 max
Call network
27 nodes / 18 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
9,898
Files
119
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
26
Internal functions
1
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 30includes a package overview page
- Examples that run
- 95%21 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 85%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- NanoTube Vignette HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
2 practices detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| ExamplePathways | list | 30 elements | No other package |
| ExampleResults | MArrayLM | 26 elements | No other package |
| GSE117751_design_matrix | data.frame | 42 × 5 | No other package |
| GSE117751_expression_matrix | data.frame | 457 × 45 | No other package |
| GSE117751_sample_data | data.frame | 42 × 7 | No other package |
| GSE117751_sample_data_replicates | data.frame | 42 × 8 | No other package |
| GSE117751_series_matrix | – | – | – |
Topics
People
- Caleb Class maintainer author
- Caiden Lukan contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("NanoTube")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btac762.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.