Package: stPipe
Type: Package
Title: Upstream pre-processing for Sequencing-Based Spatial
        Transcriptomics
Version: 1.3.0
Authors@R: c(person("Yang", "Xu", role=c("aut", "cre"), email="xu.ya@wehi.edu.au", comment=c(ORCID="0009-0008-3274-6516")), 
        person("Callum", "Sargeant", role=c("aut"), email="sargeant.ca@wehi.edu.au"), 
        person("Shian", "Su", role=c("aut"), email="su.s@wehi.edu.au"), 
        person("Luyi", "Tian", role=c("aut"), email="tian.l@wehi.edu.au"), 
        person("Yunshun", "Chen", role=c("ctb"), email="yuchen@wehi.edu.au"), 
        person("Matthew", "Ritchie", role=c("ctb", "fnd"), email="mritchie@wehi.edu.au"))
biocViews: ImmunoOncology, Software, Sequencing, RNASeq,
        GeneExpression, SingleCell, Visualization, SequenceMatching,
        Preprocessing, QualityControl, GenomeAnnotation, DataImport,
        Spatial, Transcriptomics, Clustering
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.
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
SystemRequirements: GNU make
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.2
URL: https://github.com/mritchielab/stPipe
BugReports: https://github.com/mritchielab/stPipe/issues/new
Suggests: knitr, plotly, BiocStyle, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: cmake libglpk-dev make libmagick++-dev gsfonts
        libbz2-dev libicu-dev liblzma-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev python3 xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:05:24 UTC
RemoteUrl: https://github.com/bioc/stPipe
RemoteRef: HEAD
RemoteSha: 287ceed10e841dece4bd6886acc006fb43096d94
NeedsCompilation: yes
Packaged: 2026-07-04 14:44:59 UTC; root
Author: Yang Xu [aut, cre] (ORCID: <https://orcid.org/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@wehi.edu.au>