Package Recipe 'bioconductor-subcellularspatialdata'

recipe bioconductor-subcellularspatialdata

Annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics.

Homepage:: https://bioconductor.org/packages/3.22/data/experiment/html/SubcellularSpatialData.html
License:: GPL (>= 3)
Recipe:: /bioconductor-subcellularspatialdata/meta.yaml

This is a data package that hosts annotated sub-cellular localised datasets from the STOmics, Xenium and CosMx platforms. Specifically, it hosts datasets analysed in the publication Bhuva et. al, 2024 titled "Library size confounds biology in spatial transcriptomics data". Raw transcript detections are hosted and functions to convert them to SpatialExperiment objects have been implemented.

package bioconductor-subcellularspatialdata¶

Versions:

1.6.0-0

Depends:

on bioconductor-data-packages >=20260207
on bioconductor-spatialexperiment >=1.20.0,<1.21.0
on curl
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-hexbin
on r-matrix

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-subcellularspatialdata

to add into an existing workspace instead, run:

pixi add bioconductor-subcellularspatialdata

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-subcellularspatialdata

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-subcellularspatialdata

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-subcellularspatialdata:<tag>

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