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
pathlinkR can be installed from this Github repository via devtools, or from Bioconductor as follows:
# Github development
devtools::install_github("https://github.com/hancockinformatics/pathlinkR")
# Bioconductor release
BiocManager::install("pathlinkR")
# Bioconductor develelopment
BiocManager::install("pathlinkR", version="devel")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
- A combined interface to multiple pathway enrichment tools, including
Reactome pathways and
MSigDB Hallmark
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.
pathlinkR was created and developed by Andy An & Travis Blimkie at the CMDR REW Hancock Lab.
This package follows Bioconductor's guidelines on version numbering; more information can be found here.
This project uses the GNU General Public License v3.0, available here.
