recipe bioconductor-scider

Spatial cell-type inter-correlation by density in R

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-scider/meta.yaml

scider is an user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.

package bioconductor-scider

versions:

1.0.0-0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-spatialexperiment:

>=1.12.0,<1.13.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-igraph:

depends r-isoband:

depends r-janitor:

depends r-knitr:

depends r-lwgeom:

depends r-pheatmap:

depends r-plotly:

depends r-rlang:

depends r-sf:

depends r-shiny:

depends r-spatstat.explore:

depends r-spatstat.geom:

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-scider

and update with::

   mamba update bioconductor-scider

To create a new environment, run:

mamba create --name myenvname bioconductor-scider

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-scider:<tag>

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

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-scider/README.html)