recipe bioconductor-moleculeexperiment

Prioritising a molecule-level storage of Spatial Transcriptomics Data

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-moleculeexperiment/meta.yaml

MoleculeExperiment contains functions to create and work with objects from the new MoleculeExperiment class. We introduce this class for analysing molecule-based spatial transcriptomics data (e.g., Xenium by 10X, Cosmx SMI by Nanostring, and Merscope by Vizgen). This allows researchers to analyse spatial transcriptomics data at the molecule level, and to have standardised data formats accross vendors.

package bioconductor-moleculeexperiment

versions:

1.2.2-0,  1.0.1-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-ebimage:

>=4.44.0,<4.45.0

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 r-base:

>=4.3,<4.4.0a0

depends r-cli:

depends r-data.table:

depends r-dplyr:

>=1.1.1

depends r-ggplot2:

depends r-magrittr:

depends r-matrix:

depends r-purrr:

depends r-rjson:

depends r-rlang:

depends r-terra:

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-moleculeexperiment

and update with::

   mamba update bioconductor-moleculeexperiment

To create a new environment, run:

mamba create --name myenvname bioconductor-moleculeexperiment

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-moleculeexperiment:<tag>

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

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