Package Recipe 'bioconductor-mslp'

recipe bioconductor-mslp

Predict synthetic lethal partners of tumour mutations

Homepage:: https://bioconductor.org/packages/3.20/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:

1.12.0-0, 1.8.0-0, 1.4.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-org.hs.eg.db >=3.22.0,<3.23.0
on bioconductor-rankprod >=3.36.0,<3.37.0
on r-base >=4.5,<4.6.0a0
on r-data.table >=1.13.0
on r-dorng
on r-fmsb
on r-foreach
on r-magrittr
on r-proc
on r-randomforest

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-mslp

to add into an existing workspace instead, run:

pixi add bioconductor-mslp

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-mslp

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mslp

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-mslp:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-mslp/README.html)