recipe bioconductor-ideal

Interactive Differential Expression AnaLysis






This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package.

package bioconductor-ideal

(downloads) docker_bioconductor-ideal



depends bioconductor-annotationdbi:


depends bioconductor-biocparallel:


depends bioconductor-deseq2:


depends bioconductor-genomicranges:


depends bioconductor-go.db:


depends bioconductor-goseq:


depends bioconductor-gostats:


depends bioconductor-ihw:


depends bioconductor-iranges:


depends bioconductor-limma:


depends bioconductor-pcaexplorer:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends bioconductor-topgo:


depends r-base:


depends r-base64enc:

depends r-dplyr:

depends r-dt:

depends r-ggplot2:


depends r-ggrepel:

depends r-gplots:

depends r-heatmaply:

depends r-knitr:

depends r-pheatmap:

depends r-plotly:

depends r-rentrez:

depends r-rintrojs:

depends r-rlang:

depends r-rmarkdown:

depends r-shiny:


depends r-shinyace:

depends r-shinybs:

depends r-shinydashboard:

depends r-stringr:

depends r-upsetr:



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-ideal

and update with::

   mamba update bioconductor-ideal

To create a new environment, run:

mamba create --name myenvname bioconductor-ideal

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<tag>

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

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