recipe bioconductor-hd2013sgi

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

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/HD2013SGI.html

License:

Artistic-2.0

Recipe:

/bioconductor-hd2013sgi/meta.yaml

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

versions:
1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0, 

1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.0-0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-ebimage:

>=4.44.0,<4.45.0

depends bioconductor-geneplotter:

>=1.80.0,<1.81.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-splots:

>=1.68.0,<1.69.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-gplots:

depends r-lsd:

depends r-rcolorbrewer:

depends r-vcd:

requirements:

Installation

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 quay.io/biocontainers/bioconductor-hd2013sgi:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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