recipe bioconductor-glimma

Interactive visualizations for gene expression analysis

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/Glimma.html

License:

GPL-3

Recipe:

/bioconductor-glimma/meta.yaml

Links:

biotools: glimma, doi: 10.1101/096107

This package produces interactive visualizations for RNA-seq data analysis, utilizing output from limma, edgeR, or DESeq2. It produces interactive htmlwidgets versions of popular RNA-seq analysis plots to enhance the exploration of analysis results by overlaying interactive features. The plots can be viewed in a web browser or embedded in notebook documents.

package bioconductor-glimma

versions:

2.12.0-0,  2.10.0-0,  2.8.0-0,  2.4.0-0,  2.2.0-0,  2.0.0-1,  2.0.0-0,  1.16.0-0,  1.14.0-0, 

2.12.0-0,  2.10.0-0,  2.8.0-0,  2.4.0-0,  2.2.0-0,  2.0.0-1,  2.0.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.1-0,  1.10.0-0,  1.8.2-0,  1.6.0-0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-htmlwidgets:

depends r-jsonlite:

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-glimma

and update with::

   mamba update bioconductor-glimma

To create a new environment, run:

mamba create --name myenvname bioconductor-glimma

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-glimma:<tag>

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

Download stats

Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-glimma/README.html)