proActiv
Bioc currentEstimate Promoter Activity from RNA-Seq data
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
36 8 exported
Complexity
2.6 avg / 11 max
Call network
36 nodes / 34 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
3,023
Files
108
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
20
Internal functions
28
Testing & CI
Has tests
Yes
Test-to-code ratio
1.02
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
95%
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
4.0.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2020-10-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 89%
- References docs
- 0%
Topics
Depended on by (1)
Bioconductor (1)
People
- Joseph Lee maintainer
- Deniz Demircioglu author
- Jonathan Göke author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("proActiv")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.