Package Recipe 'bioconductor-piano'

recipe bioconductor-piano

Platform for integrative analysis of omics data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/piano.html
License:: GPL (>=2)
Recipe:: /bioconductor-piano/meta.yaml
Links:: biotools: piano

Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.

package bioconductor-piano¶

Versions:

2.26.0-0, 2.22.0-0, 2.18.0-0, 2.16.0-0, 2.14.0-0, 2.10.0-0, 2.8.0-0, 2.6.0-1, 2.6.0-0,

2.26.0-0, 2.22.0-0, 2.18.0-0, 2.16.0-0, 2.14.0-0, 2.10.0-0, 2.8.0-0, 2.6.0-1, 2.6.0-0, 2.4.0-0, 2.2.0-0, 2.0.2-0, 1.22.0-0, 1.20.1-0, 1.18.0-0, 1.16.4-0, 1.12.1-0

Depends:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-fgsea >=1.36.0,<1.37.0
on bioconductor-marray >=1.88.0,<1.89.0
on r-base >=4.5,<4.6.0a0
on r-dt
on r-gplots
on r-htmlwidgets
on r-igraph
on r-relations
on r-scales
on r-shiny
on r-shinydashboard
on r-shinyjs
on r-visnetwork

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-piano

to add into an existing workspace instead, run:

pixi add bioconductor-piano

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-piano

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-piano

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-piano:<tag>

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