SiPSiC
Bioc currentCalculate Pathway Scores for Each Cell in scRNA-Seq Data
Release Lineage
Entered 3.17 · Apr 26, 2023
Current · Requires R 4.6
Description
Infer biological pathway activity of cells from single-cell RNA-sequencing data by calculating a pathway score for each cell (pathway genes are specified by the user). It is recommended to have the data in Transcripts-Per-Million (TPM) or Counts-Per-Million (CPM) units for best results. Scores may change when adding cells to or removing cells off the data. SiPSiC stands for Single Pathway analysis in Single Cells.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
2 1 exported
Complexity
2.5 avg / 3 max
Call network
2 nodes / 0 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
272
Files
12
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
1
Internal functions
1
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
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
–
System requirements
–
C++ standard
–
License
file LICENSE
License flags
SPDX valid, not OSI
History
Versions
7
First release
2023-08-16
Latest release
2026-04-28
Avg cadence
175 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
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 67%
Topics
Depended on by (1)
Bioconductor (1)
People
- Daniel Davis author maintainer
- Yotam Drier author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SiPSiC")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 v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.