profileplyr
Bioc currentVisualization and annotation of read signal over genomic ranges with profileplyr
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
26 7 exported
Complexity
13.5 avg / 120 max
Call network
26 nodes / 27 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
5,683
Files
54
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
18
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.01
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-05-12
Latest release
2026-06-04
Avg cadence
186 days
Cold removal rate
–
Dep drift
16
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 27
- Examples that run
- 88%14 run in a plain check · 2 hold no code
- Exported functions with examples
- 93%
- Documented parameters
- 96%
- Return-value docs
- 100%
- Help pages citing references
- 0%
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 |
|---|---|---|---|
| K27ac_GRlist_hind_liver_top5000 | – | – | – |
| chipExampleBig | – | – | – |
| gene_list_character | list | 2 elements | No other package |
| gene_list_dataframe | list | 2 elements | No other package |
| ik_Profiles | – | – | – |
Topics
People
- Doug Barrows author maintainer
- Tom Carroll author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("profileplyr")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 v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.