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CatsCradle
This is the released version of CatsCradle; for the devel version, see CatsCradle.
This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters
Bioconductor version: Release (3.22)
This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes.
Author: Anna Laddach [aut] ORCID iD ORCID: 0000-0001-5552-6534 , Michael Shapiro [aut, cre] ORCID iD ORCID: 0000-0002-2769-9320
Maintainer: Michael Shapiro <michael.shapiro at crick.ac.uk>
citation("CatsCradle")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CatsCradle")
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("CatsCradle")
Details
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Package Archives
Follow Installation instructions to use this package in your R session.