# 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=devel) <!-- 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. Check out our article in PLOS Computational Biology: <https://doi.org/10.1371/journal.pcbi.1012422> ## Installation **pathlinkR** can be installed from this Github repository via devtools, or from Bioconductor as follows: ```r # Github development devtools::install_github("https://github.com/hancockinformatics/pathlinkR") # Bioconductor release BiocManager::install("pathlinkR") # Bioconductor develelopment 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](https://hancockinformatics.github.io/pathlinkR/) 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 follows Bioconductor's guidelines on version numbering; more information can be found [here](https://contributions.bioconductor.org/versionnum.html). ## License This project uses the GNU General Public License v3.0, available [here](https://github.com/hancockinformatics/pathlinkR?tab=GPL-3.0-1-ov-file#readme). <br> [<img src="man/figures/hancock_lab_logo.svg" height="40px">](https://cmdr.ubc.ca/bobh/)