recipe bioconductor-mslp

Predict synthetic lethal partners of tumour mutations

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/mslp.html

License:

GPL-3

Recipe:

/bioconductor-mslp/meta.yaml

An integrated pipeline to predict the potential synthetic lethality partners (SLPs) of tumour mutations, based on gene expression, mutation profiling and cell line genetic screens data. It has builtd-in support for data from cBioPortal. The primary SLPs correlating with muations in WT and compensating for the loss of function of mutations are predicted by random forest based methods (GENIE3) and Rank Products, respectively. Genetic screens are employed to identfy consensus SLPs leads to reduced cell viability when perturbed.

package bioconductor-mslp

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends bioconductor-rankprod:

>=3.28.0,<3.29.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

>=1.13.0

depends r-dorng:

depends r-fmsb:

depends r-foreach:

depends r-magrittr:

depends r-proc:

depends r-randomforest:

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-mslp

and update with::

   mamba update bioconductor-mslp

To create a new environment, run:

mamba create --name myenvname bioconductor-mslp

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-mslp:<tag>

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

Download stats

Link to this page

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