CATALYST
Bioc currentCytometry dATa anALYSis Tools
Release Lineage
Entered 3.5 · Apr 25, 2017
Current · Requires R 4.6
Description
CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
83 34 exported
Complexity
5.9 avg / 30 max
Call network
83 nodes / 152 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
12,696
Files
122
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
44
Internal functions
49
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.28
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
4.6
System requirements
–
C++ standard
–
License
GPL (>=2)
License flags
not SPDX, not OSI
History
Versions
19
First release
2017-05-13
Latest release
2026-04-28
Avg cadence
173 days
Cold removal rate
100%
Dep drift
44
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 36
- Examples that run
- 100%36 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 89%
- Return-value docs
- 100%
- Help pages citing references
- 64%
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/helenalc/catalyst on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2018-05-16 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| PBMC_fs | – | – | – |
| PBMC_md | data.frame | 8 × 4 | No other package |
| PBMC_panel | data.frame | 24 × 3 | No other package |
| isotope_list | list | 52 elements | No other package |
| merging_table | tibble | 20 × 2 | No other package |
| mp_cells | – | – | – |
| raw_data | – | – | – |
| sample_ff | – | – | – |
| sample_key | data.frame | 20 × 6 | No other package |
| ss_exp | – | – | – |
Topics
Depended on by (4)
Bioconductor (4)
People
- Helena L. Crowell author maintainer
- Bernd Bodenmiller funder
- Stéphane Chevrier author data contributor
- Mark D. Robinson author funder
- Vito R.T. Zanotelli author
Cite
Cite this package
Run in R for the authors' entry:
citation("CATALYST")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1016/j.cels.2018.02.010, 10.12688/f1000research.11622.3, 10.12688/f1000research.26073.2.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.