TBSignatureProfiler
Bioc currentProfile RNA-Seq Data Using TB Pathway Signatures
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates known signatures and provides computational tools to enlist their usage on other datasets. The TBSignatureProfiler makes it easy to profile RNA-Seq data using these signatures and includes common signature profiling tools including ASSIGN, GSVA, and ssGSEA. Original models for some gene signatures are also available. A shiny app provides some functionality alongside for detailed command line accessibility.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
37 17 exported
Complexity
8 avg / 23 max
Call network
37 nodes / 26 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
7,081
Files
82
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
17
Internal functions
20
Testing
Has tests
Yes
Test-to-code ratio
0.30
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
9.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
13
First release
2020-04-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
19
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 40
- Examples that run
- 100%27 run in a plain check (1 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 8%
Repository practices
3 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/wejlab/tbsignatureprofiler on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| COVIDsignatures | list | 47 elements | No other package |
| OriginalTrainingData | list | 9 elements | No other package |
| TB_hiv | – | – | – |
| TB_indian | – | – | – |
| TBcommon | list | 80 elements | No other package |
| TBsignatures | list | 80 elements | No other package |
| TBsignaturesSplit | list | 7 elements | No other package |
| common_sigAnnotData | data.frame | 80 × 3 | No other package |
| sigAnnotData | data.frame | 80 × 3 | No other package |
Topics
Suggested by (1)
People
- Kiloni Quiles maintainer
- David Jenkins author org
- W. Evan Johnson author
- Christian Love contributor
- Aubrey R. Odom author dtm
- Xutao Wang author
- Yue Zhao contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("TBSignatureProfiler")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12879-020-05598-z.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.