recipe bioconductor-spotclean

SpotClean adjusts for spot swapping in spatial transcriptomics data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-spotclean/meta.yaml

SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.

package bioconductor-spotclean

versions:

1.4.1-0,  1.2.0-0,  1.0.0-0

depends bioconductor-rhdf5:

>=2.46.0,<2.47.0

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-dplyr:

depends r-ggplot2:

depends r-matrix:

depends r-rcolorbrewer:

depends r-readbitmap:

depends r-rjson:

depends r-rlang:

depends r-seurat:

depends r-tibble:

depends r-viridis:

requirements:

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-spotclean

and update with::

   mamba update bioconductor-spotclean

To create a new environment, run:

mamba create --name myenvname bioconductor-spotclean

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-spotclean:<tag>

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