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 clustersBioconductor version: Release (3.21)
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: 0000-0001-5552-6534 , Michael Shapiro [aut, cre] ORCID: 0000-0002-2769-9320
Maintainer: Michael Shapiro <michael.shapiro at crick.ac.uk>
Citation (from within R, entercitation("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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CatsCradle")Follow Installation instructions to use this package in your R session.
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