recipe bioconductor-gnosis

Genomics explorer using statistical and survival analysis in R

Homepage:

https://bioconductor.org/packages/3.18/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:

1.0.0-0

depends bioconductor-cbioportaldata:

>=2.14.0,<2.15.0

depends bioconductor-maftools:

>=2.18.0,<2.19.0

depends r-base:

>=4.3,<4.4.0a0

depends r-car:

depends r-comparegroups:

depends r-dashboardthemes:

depends r-desctools:

depends r-dt:

depends r-fabricatr:

depends r-fontawesome:

depends r-magrittr:

depends r-operator.tools:

depends r-partykit:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rpart:

depends r-rstatix:

depends r-shiny:

depends r-shinycssloaders:

depends r-shinydashboard:

depends r-shinydashboardplus:

depends r-shinyjs:

depends r-shinylogs:

depends r-shinymeta:

depends r-shinywidgets:

depends r-survival:

depends r-survminer:

depends r-tidyverse:

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-gnosis

and update with::

   mamba update bioconductor-gnosis

To create a new environment, run:

mamba create --name myenvname bioconductor-gnosis

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-gnosis:<tag>

(see `bioconductor-gnosis/tags`_ for valid values for ``<tag>``)

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Link to this page

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