neural-stem-cell-institute/screp: A Package for Enrichment Testing and Visualization of Single Cell RNA-Seq Clusters

Provides methods to visualize the results of Gene Ontology and REACTOME Pathway enrichment tests. The package also provides functions that perform the enrichment tests and prepare data frames compatible with the visualization functions. For GO enrichment, semantic similarity analysis is performed to group terms, and for the REACTOME pathway analysis, terms are grouped into the higher pathways in the tree structure from the REACTOME database website. For pathway analysis two annotations available from the REACTOME database are required. One is the ID to the pathway name, and the other is the pathway relationships to each other. The ID to pathway name file from REACTOME has several small errors (extra spaces, etc.) that can result in Na's when prepping for visualization. An easily corrected RP file for Humans is included in the package.

install.packages("remotes")
remotes::install_github("neural-stem-cell-institute/screp")