stPipe
Bioc currentUpstream pre-processing for Sequencing-Based Spatial Transcriptomics
Release Lineage
Entered 3.22 · Oct 30, 2025
Current · Requires R 4.6
Description
This package serves as an upstream pipeline for pre-processing sequencing-based spatial transcriptomics data. Functions includes FASTQ trimming, BAM file reformatting, index building, spatial barcode detection, demultiplexing, gene count matrix generation with UMI deduplication, QC, and revelant visualization. Config is an essential input for most of the functions which aims to improve reproducibility.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
27 8 exported
Complexity
4.6 avg / 20 max
Call network
27 nodes / 4 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
3,002
Files
57
Compiled share
10.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
8
Internal functions
9
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.17
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
6
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
1 externalGNU make
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2025-11-20
Latest release
2026-04-28
Avg cadence
159 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
- Help pages
- 9includes a package overview page
- Examples that run
- 100%7 run in a plain check
- Exported functions with examples
- 88%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/mritchielab/stpipe on 2026-10-18.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| Visium_Human_Transcriptome_Probe_Set_v1_0_GRCh38_2020_A | data.frame | 18,681 × 2 | No other package |
| Visium_Human_Transcriptome_Probe_Set_v2_0_GRCh38_2020_A | data.frame | 53,504 × 2 | No other package |
| Visium_Mouse_Transcriptome_Probe_Set_v1_0_mm10_2020_A | data.frame | 20,057 × 2 | No other package |
| ref_pos | data.frame | 4,991 × 6 | No other package |
| visium_v1_coordinates | data.frame | 4,992 × 3 | No other package |
| visium_v2_coordinates | data.frame | 4,992 × 3 | No other package |
| visium_v3_coordinates | data.frame | 4,992 × 3 | No other package |
| visium_v4_coordinates | data.frame | 4,992 × 3 | No other package |
| visium_v5_coordinates | data.frame | 14,336 × 3 | No other package |
Topics
People
- Yang Xu author maintainer
- Yunshun Chen contributor
- Matthew Ritchie contributor funder
- Callum Sargeant author
- Shian Su author
- Luyi Tian author
Cite
Cite this package
Run in R for the authors' entry:
citation("stPipe")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/nargab/lqaf167.
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.