recipe bioconductor-hd2013sgi

Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping






This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436.

package bioconductor-hd2013sgi

(downloads) docker_bioconductor-hd2013sgi



depends bioconductor-data-packages:


depends bioconductor-ebimage:


depends bioconductor-geneplotter:


depends bioconductor-limma:


depends bioconductor-splots:


depends curl:

depends r-base:


depends r-gplots:

depends r-lsd:

depends r-rcolorbrewer:

depends r-vcd:



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-hd2013sgi

and update with::

   mamba update bioconductor-hd2013sgi

To create a new environment, run:

mamba create --name myenvname bioconductor-hd2013sgi

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-hd2013sgi/tags`_ for valid values for ``<tag>``)

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