Analyze and interpret RNA-Seq results

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Documentation for package ‘pathlinkR’ version 1.99.42

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

.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
exampleDESeqResultsHS	List of example results from DESeq2 for human
exampleDESeqResultsMM	List of example results from DESeq2 in mice
getPathwayDistances	Calculate pairwise distances from a table of pathways and genes
groupedPathwayColours	Colour assignments for grouped pathways
hallmarkDatabaseHS	Table of Hallmark gene sets and their genes
innateDbPPIHS	InnateDB PPI data for humans
innateDbPPIMM	InnateDB PPI data for mice
keggDatabaseHS	Table of KEGG pathways and genes in humans
keggDatabaseMM	Table of KEGG pathways and genes in mice
mappingFileHS	Table of human gene ID mappings
mappingFileMM	Table of mouse gene ID mappings
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
pathwayCategoriesHS	Top-level pathway categories for human
pathwayCategoriesMM	Top-level pathway categories for mouse
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
reactomeDatabaseHS	Table of all Reactome pathways and genes for humans
reactomeDatabaseMM	Table of all Reactome pathways and genes for mice
sigoraDatabaseHS	Table of all Sigora pathways and their constituent genes for humans
sigoraDatabaseMM	Table of all Sigora pathways and their constituent genes for mice
sigoraExamplesHS	Sigora enrichment example
sigoraExamplesMM	Sigora enrichment example in mice