Given a List of Gene Symbols, Performs Differential Enrichment Analysis

Compare functional enrichment between two experimentally-derived groups of genes or proteins (Peterson, DR., et al.(2018)) . Given a list of gene symbols, 'diffEnrich' will perform differential enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. This package provides a number of functions that are intended to be used in a pipeline. Briefly, the user provides a KEGG formatted species id for either human, mouse or rat, and the package will download and clean species specific ENTREZ gene IDs and map them to their respective KEGG pathways by accessing KEGG's REST API. KEGG's API is used to guarantee the most up-to-date pathway data from KEGG. Next, the user will identify significantly enriched pathways from two gene sets, and finally, the user will identify pathways that are differentially enriched between the two gene sets. In addition to the analysis pipeline, this package also provides a plotting function.


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0.1.1 by Harry Smith, 2 years ago

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Authors: Harry Smith [aut, cre] , Laura Saba [aut]

Documentation:   PDF Manual  

GPL-2 license

Imports here, stats, rlang, stringr, reshape2, ggnewscale

Depends on dplyr, ggplot2

Suggests knitr, rmarkdown, kableExtra, diagram

See at CRAN