Package: stPipe 1.2.0

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_1.2.0.tar.gz
stPipe_1.2.0.zip(r-4.7)stPipe_1.2.0.zip(r-4.6)stPipe_1.2.0.zip(r-4.5)
stPipe_1.2.0.tgz(r-4.6-x86_64)stPipe_1.2.0.tgz(r-4.6-arm64)stPipe_1.2.0.tgz(r-4.5-x86_64)stPipe_1.2.0.tgz(r-4.5-arm64)
stPipe_1.2.0.tar.gz(r-4.7-arm64)stPipe_1.2.0.tar.gz(r-4.7-x86_64)stPipe_1.2.0.tar.gz(r-4.6-arm64)stPipe_1.2.0.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-release.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:88cc1dd7e2 (on RELEASE_3_23). Checks:12 NOTE, 1 OK, 1 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE297
linux-devel-arm64NOTE514
linux-devel-x86_64NOTE630
source / vignettesOK844
linux-release-arm64NOTE485
linux-release-x86_64NOTE663
macos-release-arm64NOTE449
macos-release-x86_64NOTE764
macos-oldrel-arm64NOTE495
macos-oldrel-x86_64NOTE788
windows-develNOTE564
windows-releaseNOTE618
windows-oldrelNOTE614
wasm-releaseFAIL261

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 30 2026.

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