Package Recipe 'bioconductor-regionalst'

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:

1.8.0-0, 1.0.1-0

Depends:

on bioconductor-bayesspace >=1.20.0,<1.21.0
on bioconductor-biocstyle >=2.38.0,<2.39.0
on bioconductor-fgsea >=1.36.0,<1.37.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-scater >=1.38.0,<1.39.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-toast >=1.24.0,<1.25.0
on r-assertthat
on r-base >=4.5,<4.6.0a0
on r-colorspace
on r-dplyr
on r-ggplot2
on r-gridextra
on r-magrittr
on r-rcolorbrewer
on r-seurat
on r-shiny
on r-tibble

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-regionalst

to add into an existing workspace instead, run:

pixi add bioconductor-regionalst

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-regionalst

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-regionalst

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-regionalst:<tag>

(see bioconductor-regionalst/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-regionalst/README.html)