Repositories list

• Infectious-Disease-Adjuvant-LLM-Fine-tuning

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 29, 2026May 29, 2026

• SciMiner-Legacy

  Public
  SciMiner Legacy (v1.1) - Biomedical literature mining tool. Perl/CGI-based system for gene/protein extraction, interaction mining, and functional enrichment ana…

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 28, 2026May 28, 2026

• hurlab

  Public
  hurlab website

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 28, 2026May 28, 2026

• richStudio

  Public
  Interactive platform for functional enrichment clustering and visualization

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 19, 2026May 19, 2026

• menopause_open

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated May 11, 2026May 11, 2026

• chemfuse

  Public
  Multi-database cheminformatics suite integrating PubChem, ChEMBL, UniChem, BindingDB, Open Targets, and SureChEMBL

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 9, 2026May 9, 2026

• Vignet

  Public
  Vignet — Vaccine-focused Integrative Gene Network from PubMed literature mining using the Vaccine Ontology (VO). Sister project to Ignet.

  reactbioinformaticsmcp+ 7

  reactbioinformaticsmcppubmedviolinvaccinegene-networkliterature-miningbiobertvaccine-ontology

  JavaScript

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 7, 2026May 7, 2026

• Ignet

  Public
  Integrative Gene Network — literature-mined gene interaction database from 848K+ PubMed abstracts with BioBERT scoring, REST API, and MCP endpoint

  reactflaskbioinformatics+ 7

  reactflaskbioinformaticsmcpsystems-biologypubmedgene-networkliterature-miningbiobertvaccine-ontology

  PHP

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 7, 2026May 7, 2026

• ALS-perturbation

  Public
  ALS subtype-specific drug perturbation analysis (C1/C2/C3 + Common) — Clue.io + L1000CDS2 + TxGNN. Manuscript accompaniment.

  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 25, 2026Apr 25, 2026

• Vaxjo-LLM

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• richR

  Public
  Function Enrichment analysis and Network construction

  R

  •

  GNU General Public License v3.0

  •66 forks•00 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• CO-PICO-PECO-LLM

  Public
  CO-PICO/PECO: Condition-based Occupational PICO/PECO and its Applications for LLM extraction and Ontological Modeling of Structured Occupational Safety and Heal…

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• SCALE-ST

  Public
  Multi-Scale Learning for Histology-Based Prediction of Spatial Gene Expression

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• DPN_DREX_HumanSpatial

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 12, 2026Apr 12, 2026

• SPECTRA

  Public
  This is home for SPECTRA (SPatial Expression predicTion using histology and tRAnsformers)

  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• pdf-ocr

  Public
  Make scanned PDFs searchable using open-weight OCR vision-language models (PaddleOCR-VL, HunyuanOCR, DeepSeek-OCR-2)

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• richStudio_legacy

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 28, 2026Mar 28, 2026

• DPN_DREX

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 25, 2026Mar 25, 2026

• irb-assistant

  Public
  PHP

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• async-grant-review

  Public
  Web-based asynchronous grant review system for NIH-style peer evaluation. Supports anonymous reviewer discussions, 1-9 criteria scoring, document upload with DO…

  PHP

  •22 forks•00 stars•00 issues•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• research-pdf-renamer

  Public
  Python

  •33 forks•00 stars•00 issues•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• EpilepsyEpigenetics

  Public
  R

  •

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 8, 2026Jan 8, 2026

• richCluster

  Public
  richCluster is a fast C++ agglomerative hierarchical clustering algorithm packaged into easily callable R functions, designed to help cluster biological 'terms'…

  HTML

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 13, 2025Dec 13, 2025

• DPN_Keto

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 12, 2025Dec 12, 2025

• COVID19VAE

  Public
  HTML

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  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 6, 2025Nov 6, 2025

• ukbiobank

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 16, 2025Oct 16, 2025

• scGEN

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Oct 3, 2025Oct 3, 2025

• AllOfUs_DPN

  Public
  A project to identify relevant clinical factors associated with diabetic peripheral neuropathy using the All of Us Research data.

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 22, 2025Aug 22, 2025

• Vaccine-Adjuvant-LLM

  Public
  Vaccine Adjuvant identification from biomedical literature using LLM

  Jupyter Notebook

  •

  MIT License

  •33 forks•11 star•00 issues•00 pull requests•Updated Jul 9, 2025Jul 9, 2025

• BRFSS-ACE

  Public
  HTML

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 15, 2025Apr 15, 2025