recipe bioconductor-mpac

Multi-omic Pathway Analysis of Cancer

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/MPAC.html

License:

GPL-3

Recipe:

/bioconductor-mpac/meta.yaml

Multi-omic Pathway Analysis of Cancer (MPAC), integrates multi-omic data for understanding cancer mechanisms. It predicts novel patient groups with distinct pathway profiles as well as identifying key pathway proteins with potential clinical associations. From CNA and RNA-seq data, it determines genes’ DNA and RNA states (i.e., repressed, normal, or activated), which serve as the input for PARADIGM to calculate Inferred Pathway Levels (IPLs). It also permutes DNA and RNA states to create a background distribution to filter IPLs as a way to remove events observed by chance. It provides multiple methods for downstream analysis and visualization.

package bioconductor-mpac

versions:

1.0.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-biocsingular:

>=1.22.0,<1.23.0

depends bioconductor-bluster:

>=1.16.0,<1.17.0

depends bioconductor-complexheatmap:

>=2.22.0,<2.23.0

depends bioconductor-fgsea:

>=1.32.0,<1.33.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-scran:

>=1.34.0,<1.35.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

>=1.14.2

depends r-fitdistrplus:

>=1.1

depends r-igraph:

>=1.4.3

requirements:

additional platforms:

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-mpac

and update with::

   mamba update bioconductor-mpac

To create a new environment, run:

mamba create --name myenvname bioconductor-mpac

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-mpac:<tag>

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

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-mpac/README.html)