recipe bioconductor-doscheda

A DownStream Chemo-Proteomics Analysis Pipeline






Doscheda focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass Spectrometry data. The package provides a shiny application to run the pipeline, several visualisations and a downloadable report of an experiment.

package bioconductor-doscheda

(downloads) docker_bioconductor-doscheda



depends bioconductor-affy:


depends bioconductor-limma:


depends bioconductor-vsn:


depends r-base:


depends r-calibrate:

depends r-corrgram:

depends r-drc:

depends r-dt:

depends r-ggplot2:

depends r-gridextra:

depends r-httr:

depends r-jsonlite:

depends r-matrixstats:

depends r-prodlim:

depends r-readxl:

depends r-reshape2:

depends r-shiny:

depends r-shinydashboard:

depends r-stringr:



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-doscheda

and update with::

   mamba update bioconductor-doscheda

To create a new environment, run:

mamba create --name myenvname bioconductor-doscheda

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-doscheda/tags`_ for valid values for ``<tag>``)

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