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✨
DESCRIPTION |NEWS
card.svg |card.png
stPipe/json (API)

# 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)

immunooncology software sequencing rnaseq geneexpression singlecell visualization sequencematching preprocessing qualitycontrol genomeannotation dataimport spatial transcriptomics clustering curl openssl zlib cpp

5.38 score 6 stars 3 scripts 8 exports 242 dependencies

Last updated from:287ceed10e. Checks:5 NOTE, 1 OK, 3 FAIL, 5 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	330
linux-devel-arm64	NOTE	506
linux-devel-x86_64	NOTE	697
source / vignettes	OK	903
linux-release-arm64	NOTE	520
linux-release-x86_64	NOTE	554
macos-release-arm64	FAIL	3787
macos-release-x86_64	ERROR	609
macos-oldrel-arm64	FAIL	3738
macos-oldrel-x86_64	ERROR	708
windows-devel	ERROR	572
windows-release	ERROR	606
windows-oldrel	ERROR	571
wasm-release	FAIL	306

Exports:Run_Clustering Run_Create_Obj Run_HTML Run_Interactive Run_Loc_Match Run_QC Run_ST Run_Visualization

Dependencies:abind AnnotationDbi askpass assorthead base64enc basilisk beachmat BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel biomaRt Biostrings bit bit64 bitops blob brio bslib cachem callr caTools cigarillo cli cluster codetools commonmark cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir DEoptimR desc diffobj digest dir.expiry dotCall64 dplyr dqrng DropletUtils edgeR evaluate farver fastDummies fastmap filelock fitdistrplus flexmix FNN fontawesome forcats formatR fs futile.logger futile.options future future.apply generics GenomicAlignments GenomicRanges GGally ggplot2 ggrepel ggridges ggstats globals glue goftest gplots gridExtra gtable gtools h5mread hash HDF5Array here highr hms htmltools htmlwidgets httpuv httr httr2 ica igraph IRanges irlba isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma listenv lmtest locfit magick magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime miniUI modeltools MultiAssayExperiment nlme nnet openssl org.Hs.eg.db org.Mm.eg.db otel parallelly patchwork pbapply pbmcapply pillar pkgbuild pkgconfig pkgload plotly plyr png polyclip praise prettyunits processx progress progressr promises ps purrr R.methodsS3 R.oo R.utils R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML RCurl reshape reshape2 restfulr reticulate rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown robustbase ROCR rprojroot Rsamtools RSpectra RSQLite Rsubread rtracklayer Rtsne S4Arrays S4Vectors S7 sass scales scattermore scPipe sctransform scuttle Seqinfo Seurat SeuratObject shiny SingleCellExperiment sitmo snow sourcetools sp spam SparseArray sparseMatrixStats SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils statmod stringi stringr SummarizedExperiment survival sys tensor testthat tibble tidyr tidyselect tinytex umap utf8 uwot vctrs viridisLite waldo withr xfun XML xml2 xtable XVector yaml zoo

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

Rendered fromstPipe-vignette.Rmdusingknitr::rmarkdown

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

Help page	Topics
Perform Basic Clustering Algorithms	Run_Clustering
This function creates specified spatial transcriptomics data object for further personalized downstream analysis	Run_Create_Obj
HTML report generation in RMarkDown format	Run_HTML
Interactive Visualization for Spatial Transcriptomics Data and spot plot with save functionality	Run_Interactive
Match spatial location After Pre-Processing for Sequencing-Based Spatial Transcriptomics	Run_Loc_Match
QC Control After Upstream Pre-Processing for Sequencing-Based Spatial Transcriptomics	Run_QC
Pre-processing function for sequencing-based spatial transcriptomics	Run_ST
Visualize pre-processed sST data	Run_Visualization
stPipe: A package for pre-processing sequencing-based spatial transcriptomics data.	stPipe-package stPipe

Package: stPipe 1.3.0

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

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