scientific-gene-expression-transcriptomics

What problem does it solve?

Provides an end-to-end workflow for bulk RNA-seq transcriptomics, integrating data retrieval from GEO, preprocessing, differential expression analysis (via PyDESeq2), GTEx reference querying, eQTL lookups, and gene-set enrichment (GSEA/ORA) to enable rapid, reproducible interpretation of transcriptomic studies.

Core Features & Use Cases

• GEO dataset retrieval and preprocessing for bulk RNA-seq and microarray data.
• Differential expression analysis using DESeq2 (via PyDESeq2) and downstream enrichment analyses (GSEA/ORA).
• GTEx tissue expression context and eQTL lookups to help interpret tissue-specific patterns.
• Expression Atlas integration for baseline and differential expression exploration.
• End-to-end pipeline outputs including ranked gene lists, enrichment reports, and publication-ready plots.

Quick Start

Run the end-to-end bulk RNA-seq pipeline to fetch GEO data, preprocess counts, perform differential expression with PyDESeq2, and interpret results with GTEx references and GSEA.