stPipe
This is the development version of stPipe; for the stable release version, see stPipe.
All Bioconductor versions of stPipe
3.24 (devel), 3.23 (release), 3.22
Upstream pre-processing for Sequencing-Based Spatial Transcriptomics
Bioconductor version: 3.24 · Package version: 1.3.0
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.
Author: Yang Xu [aut, cre] 
, Callum Sargeant [aut], Shian Su [aut], Luyi Tian [aut], Yunshun Chen [ctb], Matthew Ritchie [ctb, fnd]
Maintainer: Yang Xu <xu.ya at wehi.edu.au>
Citation
From within R, enter citation("stPipe"):
Yang Xu, Callum Sargeant, Shian Su, Luyi Tian. stPipe: Upstream pre-processing for Sequencing-Based Spatial Transcriptomics. doi:10.18129/B9.bioc.stPipe, R package version 1.3.0, https://bioconductor.org/packages/stPipe.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("stPipe")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.3.0 |
| License | GPL-3 |
| URL | https://github.com/mritchielab/stPipe |
| Bug Reports | https://github.com/mritchielab/stPipe/issues/new |
| System Requirements | GNU make |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.22 (R-4.5) (less than a year) |
| Downloads rank | 1912 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DataImport, GeneExpression, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SequenceMatching, Sequencing, SingleCell, Software, Spatial, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/stPipe/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("stPipe")| stPipe: A flexible and streamlined pipeline for processing sequencing-based spatial transcriptomics data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | stPipe_1.3.0.tar.gz |
| Windows binary (x86_64) | stPipe_1.3.0.zip |
| macOS binary (arm64) | stPipe_1.3.0.tgz |
| macOS binary (x86_64) | stPipe_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/stPipe |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/stPipe |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: basilisk, data.table, DropletUtils, dplyr, ggplot2, methods, pbmcapply, reticulate, rmarkdown, Rcpp, Rhtslib, Rsubread, Rtsne, Seurat, SeuratObject, scPipe, shiny, SummarizedExperiment, SingleCellExperiment, SpatialExperiment, stats, umap, yaml
LinkingTo: Rcpp, Rhdf5lib, testthat, Rhtslib
Suggests: knitr, plotly, BiocStyle, testthat (>= 3.0.0)