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string-db

Here are 21 public repositories matching this topic...

MuhammadMuneeb007 / PhenoGeneR

A comprehensive bioinformatics pipeline for downloading and analyzing genes associated with specific phenotypes from multiple biological databases. This package provides both R scripts for gene retrieval and Python analysis tools for downstream analysis.

bioinformatics r genomics computational-biology gtex phenotypes uniprot opentargets kegg reactome disgenet disease-gene-association hpo omim gene-prioritization literature-mining string-db phenotype-to-gene

Updated Sep 25, 2026
R

PTEN-Bioinformatics-Analysis

soumojitghosh3706-source / PTEN-Bioinformatics-Analysis

Comprehensive bioinformatics analysis of the human PTEN gene and protein using publicly available databases and computational tools.

bioinformatics genomics proteomics reactome molecular-biology human-genome alphafold cancer-biology pten string-db gepia3

Updated Aug 20, 2026

s4mehotblack / ClusterME

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

gtex enrichment-analysis enrichr bioinformatics-tool decodeme string-db

Updated Dec 27, 2025
Python

Thembelitchi / Target-Repurposing-Hypothesizer

A GNN-based platform for predicting novel drug-target interactions to accelerate R&D.

gene-expression drug-discovery drug-repurposing pubchem signaling-pathways opentargets neo4j-graph chembl rag pytorch-geometric gnn pytorch-gnn heterogeneous-graph-transformer pharmaceutical-research string-db biogpt4 biochemical-feasibility ligand-to-protein

Updated Jun 12, 2026
TypeScript

Anshuman-Roy-22 / pd-netprox

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

python bioinformatics genomics reproducible-research gtex parkinsons-disease dijkstra-shortest-path network-biology substantia-nigra-pars-compacta-da-cell string-db disease-genetics

Updated Apr 2, 2026
Python

Pranavu-github / oncotarget-luad

Scientific MVP for LUAD target prioritization using knowledge graphs, GraphSAGE, and GraphRAG.

machine-learning bioinformatics ngs computational-biology tcga knowledge-graph drug-discovery lung-cancer graphsage graph-neural-networks precision-oncology target-discovery fastapi llm open-targets graphrag mcp-server string-db

Updated Aug 24, 2026
Jupyter Notebook

Danil-V-Silin / CancerPPIr

R workflow for patient-specific protein-protein interaction subnetwork profiling from bulk RNA-seq-derived gene tables.

bioinformatics r reproducible-research louvain cancer-research network-biology bulk-rna-seq protein-protein-interactions string-db

Updated Aug 31, 2026
R

berntpopp / stringdb-link

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

bioinformatics mcp proteomics protein-protein-interaction claude network-biology functional-enrichment llm-tools model-context-protocol mcp-server fastmcp string-db genefoundry

Updated Nov 2, 2026
Python

MK0B3 / ProVisual

Protein evidence workbench — joins UniProt, STRING & Gene Ontology into one annotated report, with in-browser Kyte-Doolittle prediction and an LLM assistant. Single HTML file, no backend.

bioinformatics protein-structure vanilla-javascript computational-biology data-visualization gene-ontology proteomics uniprot single-file string-db

Updated Aug 16, 2026
HTML

terravic / string-database-visualize-skill

Science skill and CLI for STRING Database API v12.0: protein-protein interactions, functional pathway enrichment, and interactive visualization.

Updated Sep 15, 2026
HTML

arsennysan / gene-dossier

Everything about a gene on one page: 8 public databases, AI summary, Kazakh/Russian/English. Live: gene-dossier.vercel.app

bioinformatics gene genomics gemini gtex uniprot clinvar kazakh alphafold string-db

Updated Oct 24, 2026
JavaScript

neerugantibhavana-lab2code / pancreatic-cancer-ppi-network

Identifying hub and bottleneck genes in pancreatic cancer (GSE16515) via differential expression analysis (GEO2R) and PPI network topology (STRING, Cytoscape, DAVID). Found FN1, CCNB1, CDK1 as hub genes and 11 bottleneck genes as candidate biomarkers for pancreatic ductal adenocarcinoma.

bioinformatics computational-biology gene-expression cancer-genomics cytoscape ppi-network string-db geo2r

Updated Aug 21, 2026

aposfys / als-amyloid-network-analysis

Sequence, domain and interaction-network analysis of SIGMAR1 (ALS16) against a custom BLAST database of 84 amyloid-associated proteins

bioinformatics blast als interpro clustal-omega amyloid protein-networks string-db sigmar1

Updated Oct 31, 2026
Python

DrSeed / string-ppi-hub-genes

Build a protein-protein interaction network from STRING and rank hub genes by degree centrality (the CytoHubba idea).

bioinformatics protein-interaction network-biology hub-genes string-db

Updated Aug 12, 2026
Python

subhakantrout / rosetta-engine

AI-powered drug repurposing pipeline that federates live data across 8 biomedical databases in real time, ranks candidates via DeepSeek V4 LLM analysis, and visualizes target–drug–protein networks in an interactive 3D knowledge graph.

Updated Jun 21, 2026
Python

mahasaleemi585 / -alzheimers-brain-deg-analysis

RNA-seq differential expression analysis of Alzheimer's disease brain tissue using GEO dataset GSE104704, with limma, functional enrichment, and STRING network analysis.

bioinformatics rna-seq r differential-expression alzheimers-disease limma gprofiler string-db

Updated Sep 14, 2026
R

Renhuai123 / vmouse-igfbp4

虚拟小鼠 vmouse · IGFBP4 基因扰动数据包:LINCS/DepMap/IMPC/STRING 等真实公开数据检索+富集(非预测)

bioinformatics computational-biology lincs gene-perturbation virtual-mouse depmap impc string-db igfbp4

Updated May 31, 2026
HTML

artupafnah / chitin-to-hubs

From chitin elicitation to PPI hubs: RNA-seq differential expression, enrichment, and STRING network analysis of GSE133053 (chitin vs water, 1 h).

bioinformatics rna-seq differential-expression plant-immunity ppi-networks chitin string-db

Updated Oct 18, 2026
Python

rhealynalama-bio / Cell-cell-communication

Evidence-based reconstruction of cell-to-cell communication from a human pituitary somatotroph to an adipocyte via GH1 and GHR, using Human Protein Atlas, OmniPath, STRING, and IntAct. Includes data, figures, and interpretation separated from database results.

growth-hormone ligand-receptor intact omnipath human-protein-atlas cell-communication string-db human-pituitary-somatotroph

Updated Oct 8, 2026

romanbaptista / lincs-embedding

End‑to‑end pipeline for generating context‑aware drug embeddings from LINCS L1000 using RNA‑seq preprocessing, STRING PPI networks, and GNNs, with UMAP visualisation and drug‑class neighbourhood analysis.

bioinformatics rna-seq systems-biology computational-biology gene-expression drug-discovery umap data-pipeline network-biology graph-neural-networks pytorch-geometric gnn protein-interaction-network string-db lincs-l1000

Updated May 14, 2026
Jupyter Notebook

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