recipe bioconductor-sparrow

Take command of set enrichment analyses through a unified interface

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-sparrow/meta.yaml

Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.

package bioconductor-sparrow

versions:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.1-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biocset:

>=1.16.0,<1.17.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-delayedmatrixstats:

>=1.24.0,<1.25.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-gseabase:

>=1.64.0,<1.65.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends r-babelgene:

>=21.4

depends r-base:

>=4.3,<4.4.0a0

depends r-checkmate:

depends r-circlize:

depends r-data.table:

>=1.10.4

depends r-ggplot2:

>=2.2.0

depends r-irlba:

depends r-matrix:

depends r-plotly:

>=4.9.0

depends r-viridis:

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-sparrow

and update with::

   mamba update bioconductor-sparrow

To create a new environment, run:

mamba create --name myenvname bioconductor-sparrow

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-sparrow:<tag>

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