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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| CosMx Protein Assay Data Quality Control with SpaceTrooper | HTML | R Script |
| Imaging-based Spatial Transcriptomics Data Quality Control with SpaceTrooper | HTML | R Script |
| Loading CosMx and Xenium data with SpaceTrooper | HTML | R Script |
| RNA_tutorial_vignette.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, GeneExpression, ImmunoOncology, QualityControl, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| 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 | OSTA |
| 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | SpaceTrooper_1.3.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | SpaceTrooper_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | SpaceTrooper_1.3.0.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 |