recipe bioconductor-cogeqc

Systematic quality checks on comparative genomics analyses






cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.

package bioconductor-cogeqc

(downloads) docker_bioconductor-cogeqc



depends bioconductor-biostrings:


depends bioconductor-ggtree:


depends r-base:


depends r-ggbeeswarm:

depends r-ggplot2:

depends r-igraph:

depends r-jsonlite:

depends r-patchwork:

depends r-reshape2:

depends r-rlang:

depends r-scales:



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-cogeqc

and update with::

   mamba update bioconductor-cogeqc

To create a new environment, run:

mamba create --name myenvname bioconductor-cogeqc

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

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