recipe bioconductor-gscreend

Analysis of pooled genetic screens






Package for the analysis of pooled genetic screens (e.g. CRISPR-KO). The analysis of such screens is based on the comparison of gRNA abundances before and after a cell proliferation phase. The gscreend packages takes gRNA counts as input and allows detection of genes whose knockout decreases or increases cell proliferation.

package bioconductor-gscreend

(downloads) docker_bioconductor-gscreend



depends bioconductor-biocparallel:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-fgarch:

depends r-nloptr:



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-gscreend

and update with::

   mamba update bioconductor-gscreend

To create a new environment, run:

mamba create --name myenvname bioconductor-gscreend

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

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