SpatialCPie

DOI: 10.18129/B9.bioc.SpatialCPie    

Cluster analysis of Spatial Transcriptomics data

Bioconductor version: Release (3.13)

SpatialCPie is an R package designed to facilitate cluster evaluation for spatial transcriptomics data by providing intuitive visualizations that display the relationships between clusters in order to guide the user during cluster identification and other downstream applications. The package is built around a shiny "gadget" to allow the exploration of the data with multiple plots in parallel and an interactive UI. The user can easily toggle between different cluster resolutions in order to choose the most appropriate visual cues.

Author: Joseph Bergenstraahle [aut, cre]

Maintainer: Joseph Bergenstraahle <joseph.bergenstrahle at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("SpatialCPie")

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("SpatialCPie")

 

HTML	R Script	SpatialCPie
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, RNASeq, Software, Transcriptomics
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	colorspace (>= 1.3-2), data.table (>= 1.12.2), digest (>= 0.6.21), dplyr (>= 0.7.6), ggforce (>= 0.3.0), ggiraph (>= 0.5.0), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), grid (>= 3.5.1), igraph (>= 1.2.2), lpSolve (>= 5.6.13), methods (>= 3.5.0), purrr (>= 0.2.5), readr (>= 1.1.1), rlang (>= 0.2.2), shiny (>= 1.1.0), shinycssloaders (>= 0.2.0), shinyjs (>= 1.0), shinyWidgets (>= 0.4.8), stats (>= 3.6.0), SummarizedExperiment(>= 1.10.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), tidyselect (>= 0.2.4), tools (>= 3.6.0), utils (>= 3.5.0), zeallot (>= 0.1.0)
LinkingTo
Suggests	BiocStyle(>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0)
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Build Report

Package Archives

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

Source Package	SpatialCPie_1.8.0.tar.gz
Windows Binary	SpatialCPie_1.8.0.zip
macOS 10.13 (High Sierra)	SpatialCPie_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SpatialCPie
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpatialCPie
Package Short Url	https://bioconductor.org/packages/SpatialCPie/
Package Downloads Report	Download Stats