Seqtometry
Bioc currentSignature scoring for single cell analysis
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
This package provides functions used in Seqtometry (Kousnetsov et al. 2024), a method for analyzing single cell (scRNA-seq or scATAC-seq) data via signature (gene set) enrichment scores. The Seqtometry scores may be useful for annotating or characterizing cells, either in a flow cytometry like workflow (where scores are standalone features used for progressive partitoning as described in the Seqtometry publication) or in a cluster-based workflow (as features of clusters). The exported impute function (a port of Python's MAGIC-impute, van Dijk et al. 2018), may also be useful for single cell analysis on its own.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
15 2 exported
Complexity
2.7 avg / 12 max
Call network
15 nodes / 10 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
1,161
Files
30
Compiled share
9.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
2
Internal functions
10
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.18
testthat edition
3
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
4.5.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-07-27
Latest release
2026-07-27
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 13includes a package overview page
- Examples that run
- 100%2 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Seqtometry vignette HTML
Repository practices
Checks run against github.com/hawigerlab/seqtometry on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Topics
People
- Robert Kousnetsov author maintainer
- Daniel Hawiger copyright holder funder
Cite
Cite this package
Run in R for the authors' entry:
citation("Seqtometry")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1016/j.cels.2023.12.005.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.