Package Recipe 'bioconductor-bayesspace'

recipe bioconductor-bayesspace

Clustering and Resolution Enhancement of Spatial Transcriptomes

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/BayesSpace.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-bayesspace/meta.yaml

Tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

package bioconductor-bayesspace¶

Versions:

1.20.2-0, 1.12.0-0, 1.10.1-0, 1.8.0-1, 1.8.0-0, 1.4.1-1, 1.4.1-0, 1.4.0-0, 1.2.0-0,

1.20.2-0, 1.12.0-0, 1.10.1-0, 1.8.0-1, 1.8.0-0, 1.4.1-1, 1.4.1-0, 1.4.0-0, 1.2.0-0, 1.0.0-1, 1.0.0-0

Depends:

on bioconductor-biocfilecache >=3.0.0,<3.1.0
on bioconductor-biocfilecache >=3.0.0,<3.1.0a0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biocparallel >=1.44.0,<1.45.0a0
on bioconductor-biocsingular >=1.26.0,<1.27.0
on bioconductor-biocsingular >=1.26.1,<1.27.0a0
on bioconductor-rhdf5 >=2.54.0,<2.55.0
on bioconductor-rhdf5 >=2.54.1,<2.55.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-scater >=1.38.0,<1.39.0
on bioconductor-scater >=1.38.0,<1.39.0a0
on bioconductor-scran >=1.38.0,<1.39.0
on bioconductor-scran >=1.38.0,<1.39.0a0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-arrow
on r-assertthat
on r-base >=4.5,<4.6.0a0
on r-coda
on r-dirichletreg
on r-dplyr
on r-ggplot2
on r-magrittr
on r-matrix
on r-mclust
on r-microbenchmark
on r-purrr
on r-rcpp >=1.0.4.6
on r-rcpparmadillo
on r-rcppdist
on r-rcppprogress
on r-rcurl
on r-rjson
on r-rlang
on r-scales
on r-tibble
on r-tidyr
on r-xgboost >=3.0.0

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-bayesspace

to add into an existing workspace instead, run:

pixi add bioconductor-bayesspace

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-bayesspace

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-bayesspace

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-bayesspace:<tag>

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