recipe bioconductor-spillr

Spillover Compensation in Mass Cytometry Data

Homepage:

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

License:

LGPL-3

Recipe:

/bioconductor-spillr/meta.yaml

Channel interference in mass cytometry can cause spillover and may result in miscounting of protein markers. We develop a nonparametric finite mixture model and use the mixture components to estimate the probability of spillover. We implement our method using expectation-maximization to fit the mixture model.

package bioconductor-spillr

versions:

1.2.0-0

depends bioconductor-catalyst:

>=1.30.0,<1.31.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-spatstat.univar:

depends r-tibble:

depends r-tidyr:

depends r-tidyselect:

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-spillr

and update with::

   mamba update bioconductor-spillr

To create a new environment, run:

mamba create --name myenvname bioconductor-spillr

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-spillr:<tag>

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