HCATonsilData
Bioc currentProvide programmatic access to the tonsil cell atlas datasets
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
9 6 exported
Complexity
3.6 avg / 14 max
Call network
9 nodes / 6 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
1,788
Files
65
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
3
Testing
Has tests
Yes
Test-to-code ratio
0.23
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2023-10-24
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 10
- Examples that run
- 83%5 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- HCATonsilData HTML
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/massonix/hcatonsildata on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| NBC_MBC_annotation_df | data.frame | 112,478 × 5 | No other package |
| annotations_dictionary | list | 2 elements | No other package |
| colors_20230508 | list | 10 elements | No other package |
| donor_metadata | data.frame | 17 × 8 | No other package |
| features | data.frame | 36,607 × 3 | No other package |
| metadata-tonsil-atlas-rna-v1 | data.frame | 97 × 15 | No other package |
| metadata-tonsil-atlas-rna-v2 | data.frame | 77 × 15 | No other package |
| metadata-tonsil-atlas-spatial-v2 | data.frame | 23 × 15 | No other package |
| sloglo_tabular | data.frame | 121 × 7 | No other package |
Topics
People
- Ramon Massoni-Badosa author maintainer
- Helena L. Crowell author
- Federico Marini author
- Alan O'Callaghan author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("HCATonsilData")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 v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.