SpatialCPie

DOI:10.18129/B9.bioc.SpatialCPie

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, seeSpatialCPie.

Cluster analysis of Spatial Transcriptomics data

Bioconductor version: 3.14

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

Citation (from within R, entercitation("SpatialCPie")):

Installation

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

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

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

查看文档的版本包age 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 1.10.0
In Bioconductor since BioC 3.9 (R-3.6) (3 years)
License MIT + fileLICENSE
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)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package SpatialCPie_1.10.0.tar.gz
Windows Binary SpatialCPie_1.10.0.zip
macOS 10.13 (High Sierra) SpatialCPie_1.10.0.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 //www.andersvercelli.com/packages/SpatialCPie/
Package Downloads Report Download Stats

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