SpatialCPie

DOI: 10.18129/B9.bioc.SpatialCPie    

This is the development version of SpatialCPie; to use it, please install the devel version of Bioconductor.

Cluster analysis of Spatial Transcriptomics data

Bioconductor version: Development (3.9)

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>

Citation (from within R, enter citation("SpatialCPie")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SpatialCPie", version = "3.9")

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")

 

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PDF   Reference Manual
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Text   LICENSE

Details

biocViews Clustering, RNASeq, Software, Transcriptomics
Version 0.99.101
In Bioconductor since BioC 3.9 (R-3.6)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports colorspace (>= 1.3-2), dplyr (>= 0.7.6), 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), miniUI (>= 0.1.1.1), purrr (>= 0.2.5), readr (>= 1.1.1), rlang (>= 0.2.2), scatterpie (>= 0.1.2), shiny (>= 1.1.0), stats (>= 3.5.0), SummarizedExperiment(>= 1.10.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), tidyselect (>= 0.2.4), 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)
SystemRequirements
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Build Report  

Package Archives

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

Source Package SpatialCPie_0.99.101.tar.gz
Windows Binary SpatialCPie_0.99.101.zip
Mac OS X 10.11 (El Capitan) SpatialCPie_0.99.101.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 http://bioconductor.org/packages/SpatialCPie/
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