recipe bioconductor-subcellbarcode

SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-subcellbarcode/meta.yaml

Mass-Spectrometry based spatial proteomics have enabled the proteome-wide mapping of protein subcellular localization (Orre et al. 2019, Molecular Cell). SubCellBarCode R package robustly classifies proteins into corresponding subcellular localization.

package bioconductor-subcellbarcode

versions:

1.18.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0, 

1.18.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends r-base:

>=4.3,<4.4.0a0

depends r-caret:

depends r-e1071:

depends r-ggplot2:

depends r-ggrepel:

depends r-gridextra:

depends r-networkd3:

depends r-rtsne:

depends r-scatterplot3d:

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-subcellbarcode

and update with::

   mamba update bioconductor-subcellbarcode

To create a new environment, run:

mamba create --name myenvname bioconductor-subcellbarcode

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-subcellbarcode:<tag>

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

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Link to this page

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