SpatialCPie
Cluster analysis of Spatial Transcriptomics data
Bioconductor version: Release (3.20)
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("SpatialCPie")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, RNASeq, Software, Transcriptomics |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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) |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle(>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) |
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| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpatialCPie_1.22.0.tar.gz |
| Windows Binary (x86_64) | SpatialCPie_1.22.0.zip |
| macOS Binary (x86_64) | SpatialCPie_1.22.0.tgz |
| macOS Binary (arm64) | SpatialCPie_1.22.0.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 |