recipe bioconductor-pathwaypca

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-pathwaypca/meta.yaml

pathwayPCA is an integrative analysis tool that implements the principal component analysis (PCA) based pathway analysis approaches described in Chen et al. (2008), Chen et al. (2010), and Chen (2011). pathwayPCA allows users to: (1) Test pathway association with binary, continuous, or survival phenotypes. (2) Extract relevant genes in the pathways using the SuperPCA and AES-PCA approaches. (3) Compute principal components (PCs) based on the selected genes. These estimated latent variables represent pathway activities for individual subjects, which can then be used to perform integrative pathway analysis, such as multi-omics analysis. (4) Extract relevant genes that drive pathway significance as well as data corresponding to these relevant genes for additional in-depth analysis. (5) Perform analyses with enhanced computational efficiency with parallel computing and enhanced data safety with S4-class data objects. (6) Analyze studies with complex experimental designs, with multiple covariates, and with interaction effects, e.g., testing whether pathway association with clinical phenotype is different between male and female subjects. Citations: Chen et al. (2008) <https://doi.org/10.1093/bioinformatics/btn458>; Chen et al. (2010) <https://doi.org/10.1002/gepi.20532>; and Chen (2011) <https://doi.org/10.2202/1544-6115.1697>.

package bioconductor-pathwaypca

(downloads) docker_bioconductor-pathwaypca

versions:
1.18.0-0,  1.16.1-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.3-0,  1.6.0-0,  1.4.0-0,  1.2.0-0, 

1.18.0-0,  1.16.1-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.3-0,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

depends r-base:

>=4.3,<4.4.0a0

depends r-lars:

depends r-survival:

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-pathwaypca

and update with::

   mamba update bioconductor-pathwaypca

To create a new environment, run:

mamba create --name myenvname bioconductor-pathwaypca

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-pathwaypca:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda 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-pathwaypca/README.html)