# pathlinkR <img src="man/figures/pathlinkR_logo_32.svg" align="right" height="138" /> <!-- badges: start -->  [](https://github.com/hancockinformatics/pathlinkR/actions/workflows/R-CMD-check.yaml) [](https://app.codecov.io/gh/hancockinformatics/pathlinkR?branch=main) <!-- badges: end --> ## Overview **pathlinkR** is an R package designed to facilitate analysis DE genes produced from of RNA-Seq experiments. Our aim with **pathlinkR** is to provide a number of functions/tools which can be applied to list(s) of DE genes, to help the user obtain biological insights into their results, and produce publication-ready figures to summarize these findings. ## Installation **pathlinkR** can be installed from this Github repository via devtools, or from Bioconductor as follows: ```r # devtools devtools::install_github("https://github.com/hancockinformatics/pathlinkR") # Bioconductor BiocManager::install("pathlinkR", version="devel") ``` ## Workflow & functions The functions provided in **pathlinkR** can be grouped into a number of different general approaches: - Direct visualization of differential expression results: - Volcano plots to show the transcriptomic changes in a single condition - Heatmaps to compare fold changes of groups of genes across multiple conditions - Protein-Protein Interaction (PPI) network creation and visualization, leveraging curated interaction data from [InnateDB](https://www.innatedb.com/) - A combined interface to multiple pathway enrichment tools, including [Reactome](https://reactome.org/) pathways and [MSigDB Hallmark](https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp) gene sets - Simple yet effective plots to summarize and compare these findings across multiple conditions - Pathway enrichment results can also be visualized as a network of connected pathways, with the option for static or interactive output See the vignette for an example workflow including each of the included functions, and more details on the included methods and how they may be used. ## Contributors **pathlinkR** was created and developed by Andy An & Travis Blimkie at the CMDR REW Hancock Lab. ## Versioning This package makes use of [SemVer](https://semver.org/). ## License This project uses the GNU General Public License v3.0, available [here](https://github.com/hancockinformatics/pathlinkR/blob/main/LICENSE). <br> [<img src="man/figures/hancock_lab_logo.svg" height="40px">](http://cmdr.ubc.ca/bobh/)