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]
, Benedetta Banzi [aut], Oriana Romano [ctb], Matteo Merchionni [ctb], Mattia Forcato [ctb], Silvio Bicciato [aut], Davide Risso [ctb]
Maintainer: Dario Righelli <dario.righelli at gmail.com>
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 |
| Loading CosMx and Xenium data with SpaceTrooper | HTML | R Script |
| Spatial Data Quality Control on Protein data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, GeneExpression, ImmunoOncology, QualityControl, SingleCell, Software, Spatial, Transcriptomics |
| Version | 0.99.47 |
| 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, 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_0.99.47.tar.gz |
| Windows Binary (x86_64) | SpaceTrooper_0.99.3.zip |
| macOS Binary (x86_64) | SpaceTrooper_0.99.47.tgz |
| macOS Binary (arm64) | SpaceTrooper_0.99.47.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 |