An R Package for Geneset Enrichment Workflows

A web-based application to perform Gene Set Enrichment Analysis (GSEA) using clusterProfiler and shiny R libraries

Knowledge-Graph-UI (KG-UI) is an open-source web-based user interface built for KGs stored in Neo4j. The UI features Cypher queries for viewing immediate neighbors as well as shortest paths between two entities. Additionally, the API can be extended to add other functions such as enrichment analysis, and specialized queries.

GOAT: efficient and robust identification of gene set enrichment

GSEA plots in ggplot2

Deconvolution of bulk RNA-seq data using single-cell RNA-seq data as reference

Dual Threshold Optimization compares two ranked lists of features (e.g. genes) to determine the rank threshold for each list that minimizes the hypergeometric p-value of the overlap of features. It then calculates a permutation based empirical p-value and an FDR

A set of python scripts for comparing similiarity between genesets using gene embeddings.

An R package containing multiple data sets for bioinformatics analysis

Analysis pipeline to examine how gene pleiotropy influences local adaptation in Silverleaf Sunflowers

Module for GSEA Julia Implementation

bbcRNA: An R package for facilitating RNA-Seq analysis

GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene co-expression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets.

Dual Python and R notebook that compares ouput for two methods of Gene Set Enrichment Analysis (GSEA) of GSEApy and fGSEA. The webpage version is available at the link below:

RNA sequencing, bioinformatics, and data analysis involved in the Itch project for Dr. Martha Bhattacharya's Lab at the University of Arizona