factR
Bioc currentFunctional Annotation of Custom Transcriptomes
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
factR contain tools to process and interact with custom-assembled transcriptomes (GTF). At its core, factR constructs CDS information on custom transcripts and subsequently predicts its functional output. In addition, factR has tools capable of plotting transcripts, correcting chromosome and gene information and shortlisting new transcripts.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
32 14 exported
Complexity
3.7 avg / 10 max
Call network
32 nodes / 36 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
4,013
Files
71
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
18
Testing
Has tests
Yes
Test-to-code ratio
0.11
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
100%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
file LICENSE
License flags
SPDX valid, not OSI
History
Versions
8
First release
2022-11-01
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
- 25
- Examples that run
- 100%13 run in a plain check
- Exported functions with examples
- 93%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- factR HTML
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/fursham-h/factr on 2026-10-22.
The R CMD check workflow runs on macOS
GitHub Pages site last deployed 2023-01-03 · The repository has a site deploy workflow
pkgdown site last built 2023-01-03
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| chrom_matched_query_gtf | – | – | – |
| domains.known | data.frame | 85,780 × 5 | No other package |
| domains.out | data.frame | 14,880 × 5 | No other package |
| matched_query_gtf | – | – | – |
| new_query_gtf | – | – | – |
| query_cds | – | – | – |
| query_exons | – | – | – |
| query_gtf | – | – | – |
| ref_cds | – | – | – |
| ref_exons | – | – | – |
| ref_gtf | – | – | – |
Topics
People
- Fursham Hamid author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("factR")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.