transcriptogramer
Bioc currentTranscriptional analysis based on transcriptograms
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expressions are altered.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
35 1 exported
Complexity
4.4 avg / 11 max
Call network
35 nodes / 28 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
4,650
Files
70
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
13
Internal functions
34
Recent export changes
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
33.3%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.4
System requirements
1 externalJava Runtime Environment (>= 6)
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2017-10-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 31includes a package overview page
- Examples that run
- 100%29 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 13%
Repository practices
Checks run against github.com/arthurvinx/transcriptogramer on 2026-10-25.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| DEsymbols | data.frame | 12,306 × 2 | No other package |
| GPL570 | data.frame | 37,020 × 2 | No other package |
| GSE9988 | data.frame | 27,828 × 6 | No other package |
| Hs700 | vector | 17,185 elements | No other package |
| Hs800 | vector | 14,711 elements | No other package |
| Hs900 | vector | 12,396 elements | No other package |
| HsBPTerms | data.frame | 125,465 × 2 | No other package |
| Mm700 | vector | 16,690 elements | No other package |
| Mm800 | vector | 13,655 elements | No other package |
| Mm900 | vector | 11,141 elements | No other package |
| Rn700 | vector | 17,021 elements | No other package |
| Rn800 | vector | 13,887 elements | No other package |
| Rn900 | vector | 10,788 elements | No other package |
| Sc700 | vector | 6,157 elements | No other package |
| Sc800 | vector | 5,847 elements | No other package |
| Sc900 | vector | 5,213 elements | No other package |
| association | data.frame | 648,304 × 2 | No other package |
Topics
People
- Diego Morais author maintainer
- Rodrigo Dalmolin author
Cite
Cite this package
Run in R for the authors' entry:
citation("transcriptogramer")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btz007.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.