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Bioconductor - ggspavis

ggspavis

This is the released version of ggspavis; for the devel version, see ggspavis.

Visualization functions for spatial transcriptomics data

Bioconductor version: Release (3.21)

Visualization functions for spatial transcriptomics data. Includes functions to generate several types of plots, including spot plots, feature (molecule) plots, reduced dimension plots, spot-level quality control (QC) plots, and feature-level QC plots, for datasets from the 10x Genomics Visium and other technological platforms. Datasets are assumed to be in either SpatialExperiment or SingleCellExperiment format.

Author: Lukas M. Weber [aut, cre] ORCID: 0000-0002-3282-1730 , Helena L. Crowell [aut] ORCID: 0000-0002-4801-1767 , Yixing E. Dong [aut] ORCID: 0009-0003-5115-5686

Maintainer: Lukas M. Weber <lmweberedu at gmail.com>

Citation (from within R, enter citation("ggspavis")): Installation

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


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

BiocManager::install("ggspavis")

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("ggspavis")
Details biocViews DimensionReduction, GeneExpression, QualityControl, SingleCell, Software, Spatial, Transcriptomics Version 1.14.3 In Bioconductor since BioC 3.14 (R-4.1) (3.5 years) License MIT + file LICENSE Depends ggplot2 Imports SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats System Requirements URL https://github.com/lmweber/ggspavis Bug Reports https://github.com/lmweber/ggspavis/issues See More Suggests BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork Linking To Enhances Depends On Me Imports Me Suggests Me smoothclust, HCATonsilData Links To Me Build Report Build Report Package Archives

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

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