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SpaceTrooper

This is the development version of SpaceTrooper; to use it, please install the devel version of Bioconductor.

SpaceTrooper performs Quality Control analysis of Image-Based spatial


Bioconductor version: Development (3.22)

SpaceTrooper performs Quality Control analysis using data driven GLM models of Image-Based spatial data, providing exploration plots, QC metrics computation, outlier detection. It implements a GLM strategy for the detection of low quality cells in imaging-based spatial data (Transcriptomics and Proteomics). It additionally implements several plots for the visualization of imaging based polygons through the ggplot2 package.

Author: Dario Righelli [aut, cre] ORCID iD ORCID: 0000-0003-1504-3583 , Benedetta Banzi [aut], Oriana Romano [aut], Mattia Forcato [aut], Silvio Bicciato [aut], Davide Risso [aut]

Maintainer: Dario Righelli <dario.righelli at gmail.com>

Citation (from within R, enter citation("SpaceTrooper")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SpaceTrooper")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SpaceTrooper")
introduction.html HTML R Script
Spatial Data Quality Control on Protein data HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, GeneExpression, ImmunoOncology, QualityControl, SingleCell, Software, Spatial, Transcriptomics
Version 0.99.3
In Bioconductor since BioC 3.22 (R-4.5)
License MIT + file LICENSE
Depends R (>= 4.4.0), SpatialExperiment
Imports DropletUtils, S4Vectors, SummarizedExperiment, arrow, data.table, dplyr, e1071, ggplot2, ggpubr, robustbase, scater, scuttle, sf, sfheaders, tmap, cowplot, glmnet, rhdf5, methods, rlang, SpatialExperimentIO
System Requirements
URL https://github.com/drighelli/SpaceTrooper
Bug Reports https://github.com/drighelli/SpaceTrooper/issues
See More
Suggests knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), withr, viridis
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SpaceTrooper_0.99.3.tar.gz
Windows Binary (x86_64) SpaceTrooper_0.99.3.zip
macOS Binary (x86_64) SpaceTrooper_0.99.3.tgz
macOS Binary (arm64) SpaceTrooper_0.99.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/SpaceTrooper
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpaceTrooper
Bioc Package Browser https://code.bioconductor.org/browse/SpaceTrooper/
Package Short Url https://bioconductor.org/packages/SpaceTrooper/
Package Downloads Report Download Stats