Package Recipe 'bioconductor-hipathia'

recipe bioconductor-hipathia

HiPathia: High-throughput Pathway Analysis

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

3.6.0-0, 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,

3.6.0-0, 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:

on bioconductor-annotationhub >=3.14.0,<3.15.0
on bioconductor-delayedarray >=0.32.0,<0.33.0
on bioconductor-limma >=3.62.0,<3.63.0
on bioconductor-multiassayexperiment >=1.32.0,<1.33.0
on bioconductor-preprocesscore >=1.68.0,<1.69.0
on bioconductor-s4vectors >=0.44.0,<0.45.0
on bioconductor-summarizedexperiment >=1.36.0,<1.37.0
on r-base >=4.4,<4.5.0a0
on r-coin
on r-dplyr
on r-ggplot2
on r-ggpubr
on r-igraph >=1.0.1
on r-matrixstats
on r-metbrewer
on r-reshape2
on r-servr
on r-tibble
on r-visnetwork

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-hipathia

to add into an existing workspace instead, run:

pixi add bioconductor-hipathia

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-hipathia

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-hipathia

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-hipathia:<tag>

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