Package Recipe 'bioconductor-visiumstitched'

recipe bioconductor-visiumstitched

Enable downstream analysis of Visium capture areas stitched together with Fiji

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/visiumStitched.html
License:: Artistic-2.0
Recipe:: /bioconductor-visiumstitched/meta.yaml

This package provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch the images from groups of capture areas together with Fiji. Then visiumStitched builds a SpatialExperiment object with the stitched data and makes an artificial hexagonal grid enabling the seamless use of spatial clustering methods that rely on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD, which can be used to build interactive websites for stitched SpatialExperiment objects. visiumStitched also enables casting SpatialExperiment objects as Seurat objects.

package bioconductor-visiumstitched¶

Versions:

1.2.0-0

Depends:

on bioconductor-biocbaseutils >=1.12.0,<1.13.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-dropletutils >=1.30.0,<1.31.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-spatialexperiment >=1.20.0,<1.21.0
on bioconductor-spatiallibd >=1.22.0,<1.23.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-clue
on r-dplyr
on r-imager
on r-matrix
on r-pkgcond
on r-readr
on r-rjson
on r-stringr
on r-tibble
on r-tidyr
on r-xml2

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-visiumstitched

to add into an existing workspace instead, run:

pixi add bioconductor-visiumstitched

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-visiumstitched

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-visiumstitched

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-visiumstitched:<tag>

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