About this project
Description from the program archive
clusterProfiler is an efficient package that provides a universal interface for gene functional annotation from a variety of resources and is extremely helpful in data manipulation and its visualization. The idea of integrating Pathway Commons, which is an aggregated database of molecular interactions of approximately 20 databases, brings in scope to analyze data and obtain better results. However, the data lies in GMT format due to which it requires additional functions to bind pathways with their name and gene. It is then saved in RDS format to feed the enricher() function to obtain an enrichResult object. We perform ORA and GSEA using some functions defined in R script on Pathway Commons data to support it in clusterProfiler.
With the advent of a new technique ssGSEA (single sample Gene Set Enrichment Analysis) used to quantify the activity of a specific pathway or gene set in individual sample,for example, analyzing heterogeneous samples (tumor samples), integration of ssGSEA with clusterProfiler will help in better medical analyses. Thus, using packages like GSVA(Gene set variation analysis) and GenePattern we can calculate enrichment scores in permutations and support ssGSEA in clusterProfiler.