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GSoC'23 @ NRNB - Final Work Submission
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Report - GSoC'23.md

Google Summer of Code 2023 | National Resource For Network Biology

Contributor's Information :

Project : Supporting Pathway Commons and ssGSEA in clusterProfiler

clusterProfiler provides an impressive universal interface for gene functional annotation and can access data to generate enrichment results and provide effective data interpretation.

Pathway Commons is an aggregated database of molecular interaction pathways , collected from approximately 20 databases. At present, there exists no direct way to analyze data from Pathway Commons leveraging all the functionality of clusterProfiler. The data will be fetched just by specifying the URL of the database with the help of R scripts. It is proposed to enable support for Pathway Commons database in clusterProfiler to yield advanced and more accurate enrichment results and visualizations of the data.

Single sample gene set enrichment analysis is an effective method of data interpretation that uses permutations of gene sets to calculate enrichment scores. It has use cases like detecting outliers or tumors in the medical context. This is a variation of GSEA, however, clusterprofiler currently supports only GSEA. To integrate the functionality of ssGSEA, we can use GSVA package with GenePatterns to analyze gene sets in various permutations and get more indicative enrichment scores using clusterProfiler.

Description :

nrnb/GoogleSummerOfCode#222

Repository Link :

https://github.com/YuLab-SMU/clusterProfiler

Project Proposal :

Supporting Pathway Commons and ssGSEA in clusterProfiler

Project Profile :

https://summerofcode.withgoogle.com/programs/2023/projects/GYJ9YvJD

Project Goals :

  1. Creating support for Pathway Commons in clusterProfiler : PR
    https://github.com/YuLab-SMU/clusterProfiler/blob/devel/R/pathwayCommons.R
  2. Supporting ssGSEA in clusterProfiler : PR
    https://github.com/Jigyasa-G/clusterProfiler-JG/blob/master/R/ssgsea.R

Github Links: https://github.com/Jigyasa-G/clusterProfiler-JG

Blogs ( Implementation Details ):

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