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    27 repositories

    • figure-extractor

      Public
      Flask-based service using PDFFigures 2.0 to extract figures and tables from scholarly PDFs. Features REST API, CLI, Docker support, and JSON metadata output (~1.5s/page processing). Designed for document processing and RAG pipelines.
      document-processingrag
      Python
      •0•1•0•0•Updated Jan 5, 2025Jan 5, 2025

    • pQTL

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 21, 2024Oct 21, 2024

    • paperRAG

      Public
      paperRAG is a command-line interface (CLI) tool for populating and querying a database with PDF documents
      Jupyter Notebook
      •0•2•0•0•Updated Sep 24, 2024Sep 24, 2024

    • TissueSpecificCancerRisk

      Public
      R
      •0•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • MAVEN

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 1, 2024Sep 1, 2024

    • BEACON

      Public
      R
      •0•0•0•0•Updated Aug 15, 2024Aug 15, 2024

    • MaPR

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Aug 14, 2024Aug 14, 2024

    • GetFreeCopy

      Public
      Get Free Copy: A Multi-Repository Search Platform for Biomedical Publications
      open-sciencebiorxivpublicationarxivmedrxiv
      JavaScript
      •
      MIT License
      •2•2•0•0•Updated Apr 16, 2024Apr 16, 2024

    • AIScientist

      Public
      AI-Scientist is a playground to build accessible agents for automated research to drive meaningful scientific progress that can benefit the society
      Python
      •
      MIT License
      •1•3•0•0•Updated Apr 1, 2024Apr 1, 2024

    • dementia-survival-prediction

      Public
      Machine learning models identify predictive features of patient mortality across dementia types
      Jupyter Notebook
      •
      Other
      •0•2•0•0•Updated Feb 29, 2024Feb 29, 2024

    • YoungOnsetCancer

      Public
      Analysis of YoungOnsetCancer
      R
      •
      MIT License
      •1•1•0•0•Updated Jan 23, 2024Jan 23, 2024

    • oppti

      Public
      Outlier Protein and Phosphosite Target Identifier
      R
      •1•2•0•0•Updated Mar 20, 2023Mar 20, 2023

    • Get-Free-Copy-Extension

      Public
      Chrome Extension to get free copy of research papers from various repositories
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Jan 5, 2023Jan 5, 2023

    • lab_website

      Public
      This repository contains the source code for lab pages in https://labs.icahn.mssm.edu/kuanhuanglab (https://ComputationalOmicsLab.Org directs to this ISMMS-hosted address)
      HTML
      •0•0•0•0•Updated Oct 1, 2021Oct 1, 2021

    • covid19-diagnosis-prediction

      Public
      A machine-learning based framework for predicting COVID-19 diagnosis
      Jupyter Notebook
      •2•2•0•0•Updated Jul 6, 2021Jul 6, 2021

    • SParCS

      Public
      HTML
      •3•2•0•0•Updated Apr 26, 2021Apr 26, 2021

    • IRAG-2020

      Public
      MIT License
      •0•0•0•0•Updated Apr 3, 2020Apr 3, 2020

    • TCGASecondaryPredisposition

      Public
      Discover secondary genetic predisposition in 10K cancer cases
      R
      •0•0•0•0•Updated Jul 3, 2019Jul 3, 2019

    • AeQTL

      Public
      Python
      •
      MIT License
      •3•4•0•0•Updated Jul 1, 2019Jul 1, 2019

    • GermlineSomatic

      Public
      R
      •0•0•0•0•Updated May 27, 2019May 27, 2019

    • CORE

      Public
      0•1•0•0•Updated May 24, 2019May 24, 2019

    • AncestralCancerPredisposition

      Public
      Investigate predisposing variants across ancestries.
      R
      •0•0•0•0•Updated May 1, 2019May 1, 2019

    • ImmuneProteome

      Public
      Define new immune subtypes of a cancer. Find key proteins distinguishing them.
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 7, 2019Apr 7, 2019

    • ImmunotherapyGenomicBiomarkers

      Public
      0•1•0•0•Updated Feb 28, 2019Feb 28, 2019

    • BRCAProteomicsNetwork

      Public
      R
      •0•0•0•0•Updated Feb 14, 2019Feb 14, 2019

    • SequenceVariantCallEvaluation

      Public
      Evaluate coverage and sequence variant calls and contribution to their variations from potential technical and biological effects.
      R
      •
      MIT License
      •0•0•0•0•Updated Dec 4, 2018Dec 4, 2018

    • IncidenceDriverModel

      Public
      R
      •0•0•0•0•Updated Nov 9, 2018Nov 9, 2018