recipe bioconductor-pareg

Pathway enrichment using a regularized regression approach

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-pareg/meta.yaml

Compute pathway enrichment scores while accounting for term-term relations. This package uses a regularized multiple linear regression to regress differential expression p-values obtained from multi-condition experiments on a pathway membership matrix. By doing so, it is able to incorporate additional biological knowledge into the enrichment analysis and to estimate pathway enrichment scores more robustly.

package bioconductor-pareg

versions:

1.6.0-0,  1.2.0-0

depends bioconductor-basilisk:

>=1.14.0,<1.15.0

depends bioconductor-dose:

>=3.28.0,<3.29.0

depends r-base:

>=4.3,<4.4.0a0

depends r-devtools:

depends r-dofuture:

depends r-dorng:

depends r-dplyr:

depends r-foreach:

depends r-future:

depends r-ggplot2:

depends r-ggraph:

depends r-ggrepel:

depends r-glue:

depends r-hms:

depends r-igraph:

depends r-keras:

depends r-logger:

depends r-magrittr:

depends r-matrix:

depends r-nloptr:

depends r-progress:

depends r-proxy:

depends r-purrr:

depends r-reticulate:

depends r-rlang:

depends r-stringr:

depends r-tensorflow:

>=2.2.0

depends r-tfprobability:

>=0.10.0

depends r-tibble:

depends r-tidygraph:

depends r-tidyr:

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-pareg

and update with::

   mamba update bioconductor-pareg

To create a new environment, run:

mamba create --name myenvname bioconductor-pareg

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-pareg:<tag>

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

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