gtex

Variational Auto-Encoder that generates synthetic gene expression data

A unified downloader+preprocessor for cancer genomics datasets

Pipeline: Identification of cis-regulatory elements by matrix scoring and analysis of supporting empirical biological data.

Zytome is declarative library for handling gene expression data for various data portals or datasets.

Extract, cluster and analyse gene expression patterns using GTEx data and STRING-db and Enrichr APIs

Protein-network proximity analysis for Parkinson's disease candidate prioritization using STRING and GTEx substantia nigra expression.

CFDE Lung Transcriptomics Course

tool for continuously integrated meta-resource

Multithreading, data handling, and file manipulation for the GTExSnake pipeline

Agent skill and CLI toolkit for querying, analyzing, and visualizing human RNA expression baselines and cis-eQTL regulatory associations from the GTEx Portal API V2 across 54 tissues into standalone interactive HTML dashboards.

End-to-end TWAS pipeline for Alzheimer's disease integrating Kunkle et al. (2019) GWAS summary statistics with GTEx v8 MASHR brain eQTL models to identify causal genes via cross-tissue omnibus regression and functional pathway over-representation analysis.

Isoform-resolved subcellular localization of human lncRNAs: gene-level analysis masks compartment-spanning isoforms (dry-only, GTEx + ENCODE). Code for Tani, submitted.

Interactive web viewer for TF ChIP-seq binding programs at canonical protein-coding TSSs (Ensembl GRCh38.114). Streamlit + Plotly + DuckDB; ~1,300 TFs × ~19,700 TSSs; NMF programs/archetypes, GTEx + DepMap overlays, atlas-wide TF×TF network.

COMP479 - Machine Learning final project at Loyola University Chicago.

Enformer magnitude–direction dissociation in brain expression prediction | Lee 2026 | doi:10.5281/zenodo.20754856

GWAS-eQTL colocalization pipeline: pneumonia (FinnGen DF13) x CVD gene list via GTEx v8 eQTLs — 74 gene x tissue tests, PP.H3~1 across 4 loci, no shared causal variant. Master BIAM team project

Tests whether nuclear-to-mtDNA OXPHOS expression imbalance rises with age across human tissues, whether it suppresses regeneration genes, and whether NAMPT is a druggable chokepoint

Atlas analysis for controlled-access GTEx bulk datasets

Analysis and benchmarking pipelines for IsoGraph in the aging human brain, including synthetic benchmarks, BrainSEQ and GTEx analyses, cross-cohort validation, transcript-level support, and disease-QTL colocalization.

MCP server for the GTEx Portal: tissue-specific gene expression — median and per-sample TPM, top expressed genes per tissue, and gene/transcript annotation — as typed tools for LLM agents.