recipe bioconductor-tpsvg

Thin plate models to detect spatially variable genes

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/tpSVG.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-tpsvg/meta.yaml

The goal of `tpSVG` is to detect and visualize spatial variation in the gene expression for spatially resolved transcriptomics data analysis. Specifically, `tpSVG` introduces a family of count-based models, with generalizable parametric assumptions such as Poisson distribution or negative binomial distribution. In addition, comparing to currently available count-based model for spatially resolved data analysis, the `tpSVG` models improves computational time, and hence greatly improves the applicability of count-based models in SRT data analysis.

package bioconductor-tpsvg

versions:

1.2.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-matrixgenerics:

>=1.18.0,<1.19.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-spatialexperiment:

>=1.16.0,<1.17.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-mgcv:

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-tpsvg

and update with::

   mamba update bioconductor-tpsvg

To create a new environment, run:

mamba create --name myenvname bioconductor-tpsvg

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-tpsvg:<tag>

(see `bioconductor-tpsvg/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-tpsvg/README.html)