Package Recipe 'bioconductor-geoexplorer'

recipe bioconductor-geoexplorer

GEOexplorer: a webserver for gene expression analysis and visualisation

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/GEOexplorer.html
License:: GPL-3
Recipe:: /bioconductor-geoexplorer/meta.yaml

GEOexplorer is a webserver and R/Bioconductor package and web application that enables users to perform gene expression analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).

package bioconductor-geoexplorer¶

Versions:

1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-0, 1.0.0-0

Depends:

on bioconductor-biobase >=2.66.0,<2.67.0
on bioconductor-edger >=4.4.0,<4.5.0
on bioconductor-geoquery >=2.74.0,<2.75.0
on bioconductor-impute >=1.80.0,<1.81.0
on bioconductor-limma >=3.62.0,<3.63.0
on bioconductor-sva >=3.54.0,<3.55.0
on r-base >=4.4,<4.5.0a0
on r-car
on r-dt
on r-enrichr
on r-factoextra
on r-ggplot2
on r-heatmaply
on r-htmltools
on r-httr
on r-knitr
on r-markdown
on r-pheatmap
on r-plotly
on r-r.utils
on r-readxl
on r-scales
on r-shiny
on r-shinybusy
on r-shinycssloaders
on r-shinyheatmaply
on r-stringr
on r-umap
on r-xfun
on r-xml
on r-xml2

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-geoexplorer

to add into an existing workspace instead, run:

pixi add bioconductor-geoexplorer

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-geoexplorer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-geoexplorer

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-geoexplorer:<tag>

(see bioconductor-geoexplorer/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-geoexplorer/README.html)