Package: stPipe 1.3.0

Yang Xu

stPipe: Upstream pre-processing for Sequencing-Based Spatial Transcriptomics

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.

Authors:Yang Xu [aut, cre], Callum Sargeant [aut], Shian Su [aut], Luyi Tian [aut], Yunshun Chen [ctb], Matthew Ritchie [ctb, fnd]

stPipe_1.3.0.tar.gz
stPipe_1.3.0.zip(r-4.7)stPipe_1.3.0.zip(r-4.6)stPipe_1.3.0.zip(r-4.5)
stPipe_1.3.0.tgz(r-4.6-x86_64)stPipe_1.3.0.tgz(r-4.6-arm64)stPipe_1.3.0.tgz(r-4.5-x86_64)stPipe_1.3.0.tgz(r-4.5-arm64)
stPipe_1.3.0.tar.gz(r-4.7-arm64)stPipe_1.3.0.tar.gz(r-4.7-x86_64)stPipe_1.3.0.tar.gz(r-4.6-arm64)stPipe_1.3.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
stPipe/json (API)
NEWS

# Install 'stPipe' in R:
install.packages('stPipe', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mritchielab/stpipe/issues

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • openssl– Secure Sockets Layer toolkit
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On BioConductor:stPipe-1.3.0(bioc 3.24)stPipe-1.2.0(bioc 3.23)

immunooncologysoftwaresequencingrnaseqgeneexpressionsinglecellvisualizationsequencematchingpreprocessingqualitycontrolgenomeannotationdataimportspatialtranscriptomicsclusteringcurlopensslzlibcpp

5.35 score 5 stars 3 scripts 297 downloads 8 exports 242 dependencies

Last updated from:287ceed10e. Checks:12 NOTE, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE321
linux-devel-arm64NOTE509
linux-devel-x86_64NOTE543
source / vignettesOK829
linux-release-arm64NOTE504
linux-release-x86_64NOTE514
macos-release-arm64NOTE332
macos-release-x86_64NOTE807
macos-oldrel-arm64NOTE462
macos-oldrel-x86_64NOTE940
windows-develNOTE635
windows-releaseNOTE598
windows-oldrelNOTE547
wasm-releaseFAIL277

Exports:Run_ClusteringRun_Create_ObjRun_HTMLRun_InteractiveRun_Loc_MatchRun_QCRun_STRun_Visualization

Dependencies:abindAnnotationDbiaskpassassortheadbase64encbasiliskbeachmatBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelbiomaRtBiostringsbitbit64bitopsblobbriobslibcachemcallrcaToolscigarillocliclustercodetoolscommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirDEoptimRdescdiffobjdigestdir.expirydotCall64dplyrdqrngDropletUtilsedgeRevaluatefarverfastDummiesfastmapfilelockfitdistrplusflexmixFNNfontawesomeforcatsformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicAlignmentsGenomicRangesGGallyggplot2ggrepelggridgesggstatsglobalsgluegoftestgplotsgridExtragtablegtoolsh5mreadhashHDF5Arrayherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2icaigraphIRangesirlbaisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalistenvlmtestlocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminiUImodeltoolsMultiAssayExperimentnlmennetopensslorg.Hs.eg.dborg.Mm.eg.dbotelparallellypatchworkpbapplypbmcapplypillarpkgbuildpkgconfigpkgloadplotlyplyrpngpolyclippraiseprettyunitsprocessxprogressprogressrpromisespspurrrR.methodsS3R.ooR.utilsR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLRCurlreshapereshape2restfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrobustbaseROCRrprojrootRsamtoolsRSpectraRSQLiteRsubreadrtracklayerRtsneS4ArraysS4VectorsS7sassscalesscattermorescPipesctransformscuttleSeqinfoSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsSpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsystensortestthattibbletidyrtidyselecttinytexumaputf8uwotvctrsviridisLitewaldowithrxfunXMLxml2xtableXVectoryamlzoo

stPipe: A flexible and streamlined pipeline for processing sequencing-based spatial transcriptomics data

Yang Xu

Rendered fromstPipe-vignette.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-07-04
Started: 2024-09-13