recipe bioconductor-genomicsupersignature

Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-genomicsupersignature/meta.yaml

This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package.

package bioconductor-genomicsupersignature

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.1-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-flextable:

depends r-ggplot2:

depends r-ggpubr:

depends r-irlba:

depends r-plotly:

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-genomicsupersignature

and update with::

   mamba update bioconductor-genomicsupersignature

To create a new environment, run:

mamba create --name myenvname bioconductor-genomicsupersignature

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-genomicsupersignature:<tag>

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

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Link to this page

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