scruff
Bioc currentSingle Cell RNA-Seq UMI Filtering Facilitator (scruff)
Release Lineage
Entered 3.8 · Oct 31, 2018
Current · Requires R 4.6
Description
A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
43 8 exported
Complexity
3.6 avg / 18 max
Call network
43 nodes / 59 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
4,466
Files
71
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
8
Internal functions
35
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.01
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
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
16
First release
2019-04-06
Latest release
2026-04-28
Avg cadence
180 days
Cold removal rate
–
Dep drift
4
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
- 53%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Zhe Wang author maintainer
- Joshua Campbell author
- Junming Hu author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("scruff")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.