recipe bioconductor-hipathia

HiPathia: High-throughput Pathway Analysis

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-hipathia/meta.yaml

Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway.

package bioconductor-hipathia

versions:

3.2.0-0,  3.0.2-0,  2.14.0-0,  2.10.0-0,  2.8.0-0,  2.6.0-1,  2.6.0-0,  2.4.0-0,  2.2.0-0, 

3.2.0-0,  3.0.2-0,  2.14.0-0,  2.10.0-0,  2.8.0-0,  2.6.0-1,  2.6.0-0,  2.4.0-0,  2.2.0-0,  2.0.0-1,  1.3.1-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-multiassayexperiment:

>=1.28.0,<1.29.0

depends bioconductor-preprocesscore:

>=1.64.0,<1.65.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-coin:

depends r-dplyr:

depends r-ggplot2:

depends r-ggpubr:

depends r-igraph:

>=1.0.1

depends r-matrixstats:

depends r-metbrewer:

depends r-reshape2:

depends r-servr:

depends r-tibble:

depends r-visnetwork:

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-hipathia

and update with::

   mamba update bioconductor-hipathia

To create a new environment, run:

mamba create --name myenvname bioconductor-hipathia

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-hipathia:<tag>

(see `bioconductor-hipathia/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-hipathia/README.html)