Package Recipe 'bioconductor-gedi'

recipe bioconductor-gedi

Defining and visualizing the distances between different genesets

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/GeDi.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-gedi/meta.yaml

The package provides different distances measurements to calculate the difference between genesets. Based on these scores the genesets are clustered and visualized as graph. This is all presented in an interactive Shiny application for easy usage.

package bioconductor-gedi¶

Versions:

1.6.1-0

Depends:

on bioconductor-biocfilecache >=3.0.0,<3.1.0
on bioconductor-biocneighbors >=2.4.0,<2.5.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-simona >=1.8.0,<1.9.0
on bioconductor-stringdb >=2.22.0,<2.23.0
on r-base >=4.5,<4.6.0a0
on r-bs4dash
on r-circlize
on r-cluster
on r-dplyr
on r-dt
on r-expm
on r-fontawesome
on r-ggdendro
on r-ggplot2
on r-igraph
on r-matrix
on r-plotly
on r-proxyc
on r-rcolorbrewer
on r-readxl
on r-rintrojs
on r-scales
on r-shiny
on r-shinybs
on r-shinycssloaders
on r-shinywidgets
on r-tm
on r-visnetwork
on r-wordcloud2

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-gedi

to add into an existing workspace instead, run:

pixi add bioconductor-gedi

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-gedi

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-gedi

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-gedi:<tag>

(see bioconductor-gedi/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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-gedi/README.html)