recipe bioconductor-imcdatasets

Collection of publicly available imaging mass cytometry (IMC) datasets

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/imcdatasets.html

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-imcdatasets/meta.yaml

The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images.

package bioconductor-imcdatasets

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-cytomapper:

>=1.14.0,<1.15.0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-hdf5array:

>=1.30.0,<1.31.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-spatialexperiment:

>=1.12.0,<1.13.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

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-imcdatasets

and update with::

   mamba update bioconductor-imcdatasets

To create a new environment, run:

mamba create --name myenvname bioconductor-imcdatasets

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-imcdatasets:<tag>

(see `bioconductor-imcdatasets/tags`_ for valid values for ``<tag>``)

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