Package Recipe 'bioconductor-pathlinkr'

recipe bioconductor-pathlinkr

Analyze and interpret RNA-Seq results

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/pathlinkR.html
License:: GPL-3 + file LICENSE
Recipe:: /bioconductor-pathlinkr/meta.yaml

pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.

package bioconductor-pathlinkr¶

Versions:

1.6.0-0

Depends:

on bioconductor-clusterprofiler >=4.18.0,<4.19.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-fgsea >=1.36.0,<1.37.0
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-dplyr
on r-ggforce
on r-ggplot2
on r-ggpubr
on r-ggraph
on r-ggrepel
on r-igraph
on r-purrr
on r-sigora
on r-stringr
on r-tibble
on r-tidygraph
on r-tidyr
on r-vegan
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-pathlinkr

to add into an existing workspace instead, run:

pixi add bioconductor-pathlinkr

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-pathlinkr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-pathlinkr

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-pathlinkr:<tag>

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