monocle
Bioc currentClustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Release Lineage
Entered 3.0 · Oct 14, 2014
Current · Requires R 4.6
Description
Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
139 61 exported
Complexity
5.5 avg / 34 max
Call network
139 nodes / 165 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
17,342
Files
158
Compiled share
0.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
61
Internal functions
70
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.17
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
30.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.10.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
24
First release
2014-10-13
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
100%
Dep drift
21
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 78
- Examples that run
- 0%30 never run · 1 hold no code
- Exported functions with examples
- 47%
- Documented parameters
- 95%
- Return-value docs
- 86%
- Help pages citing references
- 1%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
1 practice detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| lung_exprs_data | matrix | 218 × 185 | No other package |
| lung_feature_data | data.frame | 218 × 8 | No other package |
| lung_phenotype_data | data.frame | 185 × 28 | No other package |
| spike_df | data.frame | 92 × 7 | No other package |
Topics
Depended on by (4)
Suggested by (4)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("monocle")The package provides a citation file, so citation() returns the authors' own entry.
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.