CuratedAtlasQueryR
Bioc currentQueries the Human Cell Atlas
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
22 5 exported
Complexity
1.6 avg / 4 max
Call network
22 nodes / 20 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
2,285
Files
76
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
7
Internal functions
17
Testing & CI
Has tests
Yes
Test-to-code ratio
0.21
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
8.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2023-12-07
Latest release
2026-04-28
Avg cadence
181 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
- Examples that run
- 64%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Stefano Mangiola author maintainer rev
- NHMRC 1116955 fnd
- NIH NHGRI 5U24HG004059-18 fnd
- Silicon Valley Foundation CZF2019-002443 fnd
- Vincent Carey contributor rev
- Victoria Cancer Agency ECRF21036 fnd
- Julie Iskander rev
- Michael Milton author rev
- Martin Morgan contributor rev
- Tony Papenfuss rev
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("CuratedAtlasQueryR")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.