monaLisa
Bioc currentBinned Motif Enrichment Analysis and Visualization
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
61 26 exported
Complexity
6.3 avg / 41 max
Call network
61 nodes / 134 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
12,454
Files
92
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
27
Internal functions
35
Testing
Has tests
Yes
Test-to-code ratio
0.33
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
20%
Unsafe pattern score
0
Dep constraint coverage
7.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 38 (12 internal)includes a package overview page
- Examples that run
- 100%26 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 92%
- Return-value docs
- 100%
- Help pages citing references
- 5%
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/fmicompbio/monalisa on 2026-10-18.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-06-13 · The repository has a site deploy workflow
pkgdown site last built 2026-06-13
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| LMRsESNPmerged.gr | – | – | – |
| atac_liver_vs_lung | – | – | – |
| homer_output | – | – | – |
| results.binned_6mer_enrichment_LMRs | – | – | – |
| results.binned_motif_enrichment_LMRs | – | – | – |
Topics
People
- Michael Stadler author maintainer
- Lukas Burger author
- Dania Machlab author
- Dany Mukesha contributor
- Charlotte Soneson author
Cite
Cite this package
Run in R for the authors' entry:
citation("monaLisa")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btac102.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.