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:

1.0.0-0

depends bioconductor-ebimage:

>=4.48.0,<4.49.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-spatialexperiment:

>=1.16.0,<1.17.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-abind:

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

depends r-geometry:

depends r-ggplot2:

depends r-igraph:

depends r-matrix:

depends r-msigdbr:

depends r-networkd3:

depends r-pheatmap:

depends r-pracma:

depends r-rdist:

depends r-reshape2:

depends r-rfast:

depends r-seurat:

>=5.0.1

depends r-seuratobject:

depends r-stringr:

requirements:

additional platforms:

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-catscradle

and update with::

   mamba update bioconductor-catscradle

To create a new environment, run:

mamba create --name myenvname bioconductor-catscradle

with myenvname being 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-catscradle:<tag>

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

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