CatsCradle
This is the development version of CatsCradle; for the stable release version, see CatsCradle.
This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters
Bioconductor version: Development (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:
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")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")| CatsCradle | HTML | R Script |
| CatsCradle Example Data | HTML | R Script |
| CatsCradle Quick Start | HTML | R Script |
| CatsCradle SingleCellExperiment Quick Start | HTML | R Script |
| CatsCradle Spatial Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiologicalQuestion, GeneExpression, SingleCell, Software, Spatial, StatisticalMethod, Transcriptomics |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | Seurat (>= 5.0.1), ggplot2, networkD3, stringr, pracma, reshape2, rdist, igraph, geometry, Rfast, data.table, abind, pheatmap, EBImage, S4Vectors, SeuratObject, SingleCellExperiment, SpatialExperiment, Matrix, methods, SummarizedExperiment, msigdbr |
| System Requirements | |
| URL | https://github.com/AnnaLaddach/CatsCradle |
| Bug Reports | https://github.com/AnnaLaddach/CatsCradle/issues |
See More
| Suggests | fossil, interp, knitr, BiocStyle, tictoc |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CatsCradle_1.1.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/CatsCradle |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CatsCradle |
| Bioc Package Browser | https://code.bioconductor.org/browse/CatsCradle/ |
| Package Short Url | https://bioconductor.org/packages/CatsCradle/ |
| Package Downloads Report | Download Stats |