# Analyze and interpret RNA-Seq results

## Documentation for package ‘pathlinkR’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

pathlinkR-package | pathlinkR
.eruptionBreaks | INTERNAL Create manual breaks/labels for volcano plots
.plotFoldChangeLegend | INTERNAL Construct heatmap legend
.runSigora | INTERNAL Wrapper around Sigora's enrichment function
.truncNeatly | INTERNAL Break long strings at spaces
eruption | Create a volcano plot of RNA-Seq results
exampleDESeqResults | List of example results from DESeq2
getPathwayDistances | Calculate pairwise distances from a table of pathways and genes
groupedPathwayColours | Colour assignments for grouped pathways
hallmarkDatabase | Table of Hallmark gene sets and their genes
innateDbPPI | InnateDB PPI data
mappingFile | Table of human gene ID mappings
pathlinkR | pathlinkR
pathnetCreate | Create a pathway network from enrichment results and a pathway interaction foundation
pathnetFoundation | Create the foundation for pathway networks using pathway distances
pathnetGGraph | Visualize enriched Reactome pathways as a static network
pathnetVisNetwork | Visualize enriched Reactome pathways as an interactive network
pathwayCategories | Top-level pathway categories
pathwayEnrichment | Test significant DE genes for enriched pathways
pathwayPlots | Plot pathway enrichment results
plotFoldChange | Create a heatmap of fold changes to visualize RNA-Seq results
ppiBuildNetwork | Construct a PPI network from input genes and InnateDB's database
ppiCleanNetwork | Clean GraphML or JSON input
ppiEnrichNetwork | Test a PPI network for enriched pathways
ppiExtractSubnetwork | Extract a subnetwork based on pathway genes
ppiPlotNetwork | Plot an undirected PPI network using ggraph
ppiRemoveSubnetworks | INTERNAL Find and return the largest subnetwork
reactomeDatabase | Table of all Reactome pathways and genes
sigoraDatabase | Table of all Sigora pathways and their constituent genes
sigoraExamples | Sigora enrichment example