Package Recipe 'bioconductor-catscradle'

recipe bioconductor-catscradle

This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/CatsCradle.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-catscradle/meta.yaml

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.

package bioconductor-catscradle¶

Versions:

1.4.2-0, 1.0.0-0

Depends:

on bioconductor-ebimage >=4.52.0,<4.53.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-spatialexperiment >=1.20.0,<1.21.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-abind
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-geometry
on r-ggplot2
on r-igraph
on r-matrix
on r-msigdbr
on r-networkd3
on r-pheatmap
on r-pracma
on r-rdist
on r-reshape2
on r-rfast
on r-seurat >=5.0.1
on r-seuratobject
on r-stringr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-catscradle

to add into an existing workspace instead, run:

pixi add bioconductor-catscradle

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-catscradle

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-catscradle

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-catscradle:<tag>

(see bioconductor-catscradle/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-catscradle/README.html)