stPipe
This is the released version of stPipe; for the devel version, see stPipe.
Upstream pre-processing for Sequencing-Based Spatial Transcriptomics
Bioconductor version: Release (3.22)
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] ORCID iD ORCID: 0009-0008-3274-6516 , 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("stPipe")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("stPipe")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("stPipe")
Details
Package Archives
Follow Installation instructions to use this package in your R session.