Package Recipe 'bioconductor-gnosis'

recipe bioconductor-gnosis

Genomics explorer using statistical and survival analysis in R

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/GNOSIS.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-gnosis/meta.yaml

GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.

package bioconductor-gnosis¶

Versions:

1.8.0-0, 1.4.0-0, 1.0.0-0

Depends:

on bioconductor-cbioportaldata >=2.22.0,<2.23.0
on bioconductor-maftools >=2.26.0,<2.27.0
on r-base >=4.5,<4.6.0a0
on r-car
on r-comparegroups
on r-dashboardthemes
on r-desctools
on r-dt
on r-fabricatr
on r-fontawesome
on r-magrittr
on r-operator.tools
on r-partykit
on r-rcolorbrewer
on r-reshape2
on r-rpart
on r-rstatix
on r-shiny
on r-shinycssloaders
on r-shinydashboard
on r-shinydashboardplus
on r-shinyjs
on r-shinylogs
on r-shinymeta
on r-shinywidgets
on r-survival
on r-survminer
on r-tidyverse

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-gnosis

to add into an existing workspace instead, run:

pixi add bioconductor-gnosis

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-gnosis

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-gnosis

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-gnosis:<tag>

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