stPipe
This is thereleased version of stPipe; for the devel version, seestPipe.
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: 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 appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("stPipe")| stPipe: A flexible and streamlined pipeline for processing sequencing-based spatial transcriptomics data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering,DataImport,GeneExpression,GenomeAnnotation,ImmunoOncology,Preprocessing,QualityControl,RNASeq,SequenceMatching,Sequencing,SingleCell,Software,Spatial,Transcriptomics,Visualization |
| Version | 1.0.1 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | GPL-3 |
| 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 |
| System Requirements | GNU make |
| URL | https://github.com/mritchielab/stPipe |
| Bug Reports | https://github.com/mritchielab/stPipe/issues/new |
See More
| Suggests | knitr,plotly,BiocStyle,testthat (>= 3.0.0) |
| Linking To | Rcpp,Rhdf5lib,testthat,Rhtslib |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | stPipe_1.0.1.tar.gz |
| Windows Binary (x86_64) | stPipe_1.0.0.zip |
| macOS Binary (x86_64) | stPipe_1.0.1.tgz |
| macOS Binary (arm64) | stPipe_1.0.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/stPipe |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/stPipe |
| Bioc Package Browser | https://code.bioconductor.org/browse/stPipe/ |
| Package Short Url | https://bioconductor.org/packages/stPipe/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.22 | Source Archive |