recipe bioconductor-topdownr

Investigation of Fragmentation Conditions in Top-Down Proteomics



GPL (>= 3)



The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

package bioconductor-topdownr

(downloads) docker_bioconductor-topdownr



depends bioconductor-biobase:


depends bioconductor-biocgenerics:


depends bioconductor-biostrings:


depends bioconductor-msnbase:


depends bioconductor-mzr:


depends bioconductor-protgenerics:


depends bioconductor-s4vectors:


depends r-base:


depends r-ggplot2:


depends r-matrix:




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-topdownr

and update with::

   mamba update bioconductor-topdownr

To create a new environment, run:

mamba create --name myenvname bioconductor-topdownr

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

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