cmapR
Bioc currentCMap Tools in R
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
The Connectivity Map (CMap) is a massive resource of perturbational gene expression profiles built by researchers at the Broad Institute and funded by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Please visit https://clue.io for more information. The cmapR package implements methods to parse, manipulate, and write common CMap data objects, such as annotated matrices and collections of gene sets.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
50 40 exported
Complexity
2.8 avg / 15 max
Call network
50 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
5,883
Files
169
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
52
Internal functions
10
Testing
Has tests
Yes
Test-to-code ratio
0.46
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
4.0
System requirements
–
C++ standard
–
License
file LICENSE
License flags
SPDX valid, not OSI
History
Versions
13
First release
2020-04-27
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
- 43 (6 internal)
- Examples that run
- 86%32 run in a plain check · 5 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- cmapR Tutorial HTML
Repository practices
Checks run against github.com/cmap/cmapr on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| cdesc_char | data.frame | 368 × 8 | No other package |
| ds | – | – | – |
| gene_set | list | 8 elements | No other package |
| kd_gct | – | – | – |
Topics
People
- Ted Natoli author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("cmapR")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 v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.