SpaceTrooper
This is the development version of SpaceTrooper; for the stable release version, see SpaceTrooper.
SpaceTrooper performs Quality Control analysis of Image-Based spatial
Bioconductor version: Development (3.24)
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] 
, Benedetta Banzi [aut], Matteo Marchionni [aut], Oriana Romano [ctb], Mattia Forcato [ctb], Silvio Bicciato [aut], Davide Risso [ctb]
Maintainer: Dario Righelli <dario.righelli at gmail.com>
citation("SpaceTrooper")):Dario Righelli, Benedetta Banzi, Matteo Marchionni, Silvio Bicciato. SpaceTrooper: SpaceTrooper performs Quality Control analysis of Image-Based spatial. doi:10.18129/B9.bioc.SpaceTrooper, R package version 1.3.1, https://bioconductor.org/packages/SpaceTrooper.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| Loading CosMx and Xenium data with SpaceTrooper | HTML | R Script |
| CosMx Protein Assay Data Quality Control with SpaceTrooper | HTML | R Script |
| RNA_tutorial_vignette.html | HTML | R Script |
| SpaceTrooper utilities overview | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, GeneExpression, ImmunoOncology, QualityControl, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.3.1 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0), SpatialExperiment |
| Imports | DropletUtils, S4Vectors, SummarizedExperiment, arrow, data.table, dplyr, e1071, ggplot2, ggpubr, robustbase, scater, scuttle, sf, sfheaders, 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpaceTrooper_1.3.1.tar.gz |
| Windows Binary (x86_64) | SpaceTrooper_1.3.1.zip |
| macOS Binary (big-sur-x86_64) | SpaceTrooper_1.3.1.tgz |
| macOS Binary (sonoma-arm64) | SpaceTrooper_1.3.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpaceTrooper |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpaceTrooper |
| Package Short Url | https://bioconductor.org/packages/SpaceTrooper/ |
| Package Downloads Report | Download Stats |