functional-enrichment

Gene Set Clustering based on Functional annotation

From functional enrichment results to biological networks

A collection of source codes for network-based multi-omics analysis using integrated genome-wide association studies (GWAS) and transcriptomic data to identify genetic contribution into lithium response in patients with bipolar disorder (BD).

Reproducible R workflow for background-aware, multi-context functional enrichment of non-model and reference-based transcriptomic datasets, integrating GOseq, g:Profiler, RRvGO, consensus scoring, and GO-term networks.

util scripts for various omics data analysis

Context-aware restriction of the Gene Ontology (GO) for enrichment analysis.

A Python script for testing over- and under-representation of Gene Ontology (GO) terms in a target gene set relative to a background set, using the hypergeometric test with Benjamini-Hochberg FDR correction.

MCP server for STRING v12: protein–protein association networks, interaction partners, and functional enrichment analysis — as typed tools for LLM agents.

Static, client-side bioinformatics tool for cross-species gene analysis centered on S. pombe. Integrates ortholog mapping, PPI networks, GO/KEGG enrichment, and phylogenetic trees across 7 model organisms — entirely in-browser, no server required. Built on STRING v12.0, KEGG, and eggNOG v7.

Genomic Interactive Plotting for GO Terms and KEGG functional enrichment results

Cross-platform (Windows + Linux) no-code desktop app for reproducible bulk RNA-seq & microarray analysis: STAR/HISAT2/Salmon alignment, DESeq2/limma, GO/KEGG/g:Profiler enrichment, and STRING PPI networks — with first-class support for crops and fungi that lack a Bioconductor OrgDb.

Interactive ATAC-seq peak analysis app in R Shiny—annotation, motif enrichment, machine learning, and more. Singularity/HPC ready.

RNA-seq analysis of FOXP1-regulated genes in a mouse hippocampus model with integration of schizophrenia GWAS data

Comprehensive RNA-seq differential expression analysis with automated Snakemake workflow, tool-specific Conda environments, and publication-style visualizations.

De novo transcriptome of Staurois parvus + DGE + FE

Explainable AI framework for breast cancer transcriptomics, biomarker discovery, molecular subtype classification, and patient-centric heterogeneity analysis.

Static, client-side Fusarium gene analysis tool: ortholog mapping, PPI networks, phylogenetic trees, and GO/KEGG enrichment across 20 species — no backend required.