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    71 repositories

    • KAZU

      Public
      Fast, world class biomedical NER
      biomedical-text-miningnlpnatural-language-processing
      Python
      •
      Apache License 2.0
      •7•77•26•9•Updated Dec 13, 2024Dec 13, 2024

    • peptide-tools

      Public
      Programs to calculate phys-chem properties of synthetic peptides and proteins: isoelectric point and extinction coefficients.
      Python
      •
      Apache License 2.0
      •5•26•0•0•Updated Dec 13, 2024Dec 13, 2024

    • persist-seq-galaxy-tools-setup

      Public
      Python
      •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • jazzy

      Public
      Fast calculation of hydrogen-bond strengths and free energy of hydration of small molecules.
      Python
      •
      Other
      •6•79•3•16•Updated Nov 29, 2024Nov 29, 2024

    • maraca

      Public
      R package for the creation of "maraca" plots
      R
      •
      Other
      •0•3•1•0•Updated Nov 29, 2024Nov 29, 2024

    • bone_challenge

      Public
      code for Bone Challenge
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 28, 2024Nov 28, 2024

    • biomedical-kg-topological-imbalance

      Public
      Code to accompany the "Implications of Topological Imbalance for Representation Learning on Biomedical Knowledge Graphs" (Briefings in Bioinformatics, 2022)
      knowledge-graphdrug-discoveryknowledge-graph-completiontarget-predictiondrug-discovery-knowledge-graph
      Jupyter Notebook
      •
      Apache License 2.0
      •0•16•0•0•Updated Nov 25, 2024Nov 25, 2024

    • Ovarian_genomics_HRD

      Public
      This repository contains the applicable source code that was used for data processing, visualisation and statistical analysis for a publication titled " Patterns of genomic instability in > 2000 patients with ovarian cancer across six clinical trials evaluating olaparib"
      R
      •
      Other
      •0•1•0•0•Updated Nov 5, 2024Nov 5, 2024

    • DiffAbXL

      Public
      The official implementation of DiffAbXL benchmarked in the paper "Exploring Log-Likelihood Scores for Ranking Antibody Sequence Designs", formerly titled "Benchmarking Generative Models for Antibody Design".
      log-likelihoodgraph-neural-networksdiffusion-modelsbinding-affinityin-silico-designgenerative-aiantibody-designllm-models
      Python
      •
      Apache License 2.0
      •6•55•0•0•Updated Oct 25, 2024Oct 25, 2024

    • runnable

      Public
      Runnable
      Python
      •
      Apache License 2.0
      •4•40•7•3•Updated Oct 19, 2024Oct 19, 2024

    • e2-bioprotac

      Public
      Bioinformatics data analyses - Taylor J. D. et al., Communications Biology 2024, doi: 10.1038/s42003-024-06803-4
      Apache License 2.0
      •0•1•0•0•Updated Sep 20, 2024Sep 20, 2024

    • persist

      Public
      This provides the necessary code and a short tutorial to run PersiST, an exploratory tool for spatial 'omics datasets.
      Python
      •1•1•0•0•Updated Aug 27, 2024Aug 27, 2024

    • kgem-in-drug-discovery

      Public
      Code to accompany the "Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery" manuscript (Artificial Intelligence in the Life Sciences, 2022)
      knowledge-graphdrug-discoveryknowledge-graph-embeddingstarget-predictionknowledge-graph-embedding-modelsdrug-discovery-knowledge-graph
      Python
      •
      Apache License 2.0
      •6•32•0•0•Updated Aug 16, 2024Aug 16, 2024

    • metabolic_classifier

      Public
      Jupyter Notebook
      •0•1•0•3•Updated Jul 30, 2024Jul 30, 2024

    • lung-tumour-mice-mri

      Public
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Jul 18, 2024Jul 18, 2024

    • MCPL

      Public
      Official implementation for "An image is worth multiple words: discovering object level concepts using multi-concepts prompts learning" [ICML 2024]]
      Python
      •
      Apache License 2.0
      •2•14•3•0•Updated Jul 16, 2024Jul 16, 2024

    • mcpl.github.io

      Public
      HTML
      •0•0•0•0•Updated Jul 16, 2024Jul 16, 2024

    • awesome-drug-discovery-knowledge-graphs

      Public
      A collection of research papers, datasets and software related to knowledge graphs for drug discovery. Accompanies the paper "A review of biomedical datasets relating to drug discovery: a knowledge graph perspective" (Briefings in Bioinformatics, 2022)
      knowledge-graphdrug-discoveryawesome-listdrug-discovery-knowledge-graph
      Apache License 2.0
      •23•212•0•0•Updated Jul 14, 2024Jul 14, 2024

    • MVDA_exploration_tools

      Public
      Multivariate data analysis (MVDA) exploration tool is a Python library utilizing the scikit-learn library for partial least squares (PLS) and principal components analysis (PCA).
      Jupyter Notebook
      •
      Apache License 2.0
      •1•5•0•0•Updated Jun 5, 2024Jun 5, 2024

    • multimodal-python-course

      Public
      The purpose of the code is to facilitate a comprehensive understanding of multimodal data science applications within medical domain. The code serves to support the delivery of a cutting-edge workshop designed to introduce researchers to the rapidly evolving field of multimodal data science
      Jupyter Notebook
      •
      Apache License 2.0
      •0•7•0•0•Updated May 19, 2024May 19, 2024

    • safeenv

      Public
      Safe R environment that raises an error if a key has never been defined, instead of returning NULL
      R
      •0•0•0•0•Updated May 7, 2024May 7, 2024

    • qsuse

      Public
      R library that provides an import mechanism like python to import local source files. It is not meant to replace library(), or doublecolon:: prefixing
      R
      •0•0•0•0•Updated May 7, 2024May 7, 2024

    • reactive6

      Public
      Reactive R6 models for Shiny
      R
      •0•1•0•0•Updated May 7, 2024May 7, 2024

    • dpp_imp

      Public
      Improved clinical data imputation via classical and quantum determinantal point processes
      Python
      •0•1•0•1•Updated Apr 3, 2024Apr 3, 2024

    • roo

      Public
      A package and environment manager for R
      Python
      •
      Apache License 2.0
      •1•12•17•5•Updated Mar 8, 2024Mar 8, 2024

    • SelfPAD

      Public
      The official implementation of "Improving Antibody Humanness Prediction using Patent Data".
      transformerattentionantibodypatent-dataantibody-sequencecontrastive-learningimmunogenicity-predictionhumannessantibody-design
      Python
      •
      Apache License 2.0
      •4•9•0•0•Updated Feb 14, 2024Feb 14, 2024

    • ConvCaps-DR

      Public
      Tensorflow-Keras implementation of deep Convolutional Capsule Networks with Dynamic Routing algorithm
      Python
      •
      Apache License 2.0
      •0•4•0•3•Updated Feb 1, 2024Feb 1, 2024

    • CKD_molecular_stratification

      Public
      R
      •
      Apache License 2.0
      •0•1•0•0•Updated Feb 1, 2024Feb 1, 2024

    • kallisto

      Public
      Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.
      chemistrycomputational-chemistryquantum-chemistrymachinelearning
      Python
      •
      Apache License 2.0
      •21•62•2•0•Updated Feb 1, 2024Feb 1, 2024

    • adhce

      Public
      R
      •
      Apache License 2.0
      •0•1•0•0•Updated Jan 19, 2024Jan 19, 2024