recipe bioconductor-regionalst

Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/RegionalST.html

License:

GPL-3

Recipe:

/bioconductor-regionalst/meta.yaml

This package analyze spatial transcriptomics data through cross-regional analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.

package bioconductor-regionalst

versions:

1.0.1-0

depends bioconductor-bayesspace:

>=1.12.0,<1.13.0

depends bioconductor-fgsea:

>=1.28.0,<1.29.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-scater:

>=1.30.0,<1.31.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-toast:

>=1.16.0,<1.17.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-colorspace:

depends r-dplyr:

depends r-ggplot2:

depends r-gridextra:

depends r-magrittr:

depends r-rcolorbrewer:

depends r-seurat:

depends r-shiny:

depends r-tibble:

requirements:

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-regionalst

and update with::

   mamba update bioconductor-regionalst

To create a new environment, run:

mamba create --name myenvname bioconductor-regionalst

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-regionalst:<tag>

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

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Link to this page

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