celaref
Bioc currentSingle-cell RNAseq cell cluster labelling by reference
Release Lineage
Entered 3.8 · Oct 31, 2018
Current · Requires R 4.6
Description
After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data).
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
28 14 exported
Complexity
4.3 avg / 12 max
Call network
28 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
6,353
Files
75
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
14
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.07
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
3.5.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
16
First release
2019-01-04
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 35
- Examples that run
- 100%12 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Manual HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| .Random.seed | vector | 626 elements | No other package |
| dataset_se.P4 | – | – | – |
| de_table.demo_query | data.frame | 800 × 13 | No other package |
| de_table.demo_ref | data.frame | 800 × 13 | No other package |
| demo_cell_info_table | data.frame | 515 × 4 | No other package |
| demo_counts_matrix | matrix | 200 × 514 | No other package |
| demo_gene_info_table | data.frame | 200 × 2 | No other package |
| demo_microarray_expr | matrix | 200 × 20 | No other package |
| demo_microarray_expression | data.frame | 200 × 20 | No other package |
| demo_microarray_info | data.frame | 20 × 2 | No other package |
| demo_microarray_sample_sheet | tibble | 20 × 2 | No other package |
| demo_query_se | – | – | – |
| demo_ref_se | – | – | – |
| samples_table | tibble | 42 × 7 | No other package |
| sim_query_cell_info | data.frame | 485 × 4 | No other package |
| sim_query_counts | data.frame | 200 × 486 | No other package |
| sim_query_gene_info | data.frame | 200 × 2 | No other package |
| sim_ref_cell_info | data.frame | 515 × 4 | No other package |
| sim_ref_counts | data.frame | 200 × 516 | No other package |
| sim_ref_gene_info | data.frame | 200 × 2 | No other package |
Topics
People
- Sarah Williams author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
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