- recipe bioconductor-spatialcpie
Cluster analysis of Spatial Transcriptomics data
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/SpatialCPie.html
- License:
MIT + file LICENSE
- Recipe:
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.
- package bioconductor-spatialcpie¶
- versions:
1.18.0-0,1.16.0-0,1.14.0-0,1.10.0-0,1.8.0-0,1.6.0-1,1.6.0-0,1.4.0-0,1.2.0-0,1.18.0-0,1.16.0-0,1.14.0-0,1.10.0-0,1.8.0-0,1.6.0-1,1.6.0-0,1.4.0-0,1.2.0-0,1.0.0-1- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends r-base:
>=4.3,<4.4.0a0- depends r-colorspace:
>=1.3-2- depends r-data.table:
>=1.12.2- depends r-digest:
>=0.6.21- depends r-dplyr:
>=0.7.6- depends r-ggforce:
>=0.3.0- depends r-ggiraph:
>=0.5.0- depends r-ggplot2:
>=3.0.0- depends r-ggrepel:
>=0.8.0- depends r-igraph:
>=1.2.2- depends r-lpsolve:
>=5.6.13- depends r-purrr:
>=0.2.5- depends r-readr:
>=1.1.1- depends r-rlang:
>=0.2.2- depends r-shiny:
>=1.1.0- depends r-shinycssloaders:
>=0.2.0- depends r-shinyjs:
>=1.0- depends r-shinywidgets:
>=0.4.8- depends r-tibble:
>=1.4.2- depends r-tidyr:
>=0.8.1- depends r-tidyselect:
>=0.2.4- depends r-zeallot:
>=0.1.0- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-spatialcpie and update with:: mamba update bioconductor-spatialcpie
To create a new environment, run:
mamba create --name myenvname bioconductor-spatialcpie
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-spatialcpie:<tag> (see `bioconductor-spatialcpie/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-spatialcpie/README.html)
