SpatialCPie

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see SpatialCPie.

Cluster analysis of Spatial Transcriptomics data


Bioconductor version: 3.10

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 (!require("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")
SpatialCPie HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, RNASeq, Software, Transcriptomics
Version 1.2.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports colorspace (>= 1.3-2), data.table (>= 1.12.2), 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)
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Suggests BiocStyle(>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0)
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Package Archives

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

Source Package SpatialCPie_1.2.0.tar.gz
Windows Binary SpatialCPie_1.2.0.zip
Mac OS X 10.11 (El Capitan) SpatialCPie_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SpatialCPie
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpatialCPie
Bioc Package Browser https://code.bioconductor.org/browse/SpatialCPie/
Package Short Url https://bioconductor.org/packages/SpatialCPie/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive