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    111 repositories

    • frequent-hitters

      Public
      Data pre-processing and chemprop model for frequent hitter prediction
      MIT License
      •0•0•0•0•Updated Jul 10, 2026Jul 10, 2026

    • orthoMTL

      Public
      R
      •0•1•0•0•Updated Jul 10, 2026Jul 10, 2026

    • synadam

      Public
      synadam is an R package that generates synthetic ADaM clinical trial datasets from real data using a glimpse-then-simulate approach. It preserves statistical pr…
      R
      •
      Other
      •0•0•0•0•Updated Jul 9, 2026Jul 9, 2026

    • Causal-inference-in-RCTs

      Public
      This repository contains code examples for several methods in a Causal Inference in RCTs short course.
      R
      •
      MIT License
      •0•27•0•0•Updated Jul 6, 2026Jul 6, 2026

    • RBesT

      Public
      Tool-set to support Bayesian evidence synthesis in R
      clinicalbayesianmeta-analysis
      clinicalbayesianmeta-analysishistorical-data
      R
      •
      GNU General Public License v3.0
      •3•25•0•0•Updated Jul 6, 2026Jul 6, 2026

    • torchsurv

      Public
      Deep survival analysis made easy
      deep-learningpytorchsurvival-analysis
      deep-learningpytorchsurvival-analysis
      Python
      •
      MIT License
      •16•209•5•2•Updated Jul 1, 2026Jul 1, 2026

    • pisces

      Public
      PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
      bioinformaticsbioinformatics-pipelinernaseq
      bioinformaticsbioinformatics-pipelinernaseqtranscriptomicssalmonrnaseq-pipeline
      Python
      •
      Apache License 2.0
      •3•30•10•2•Updated Jul 1, 2026Jul 1, 2026

    • AVIDbase

      Public
      Computational pipeline for the preparation of the AVIDbase dataset of nanobody-antigen crystal structures from the PDB.
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 17, 2026Jun 17, 2026

    • slc-localization

      Public
      The codebase created to support the application of artificial intelligence for predicting the subcellular localization of solute carrier transporter (SLC) prote…
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 12, 2026Jun 12, 2026

    • NODE

      Public
      NODE is an R package for identifying transcription factor (TF) target genes by integrating TF binding sites, 3D chromatin interactions (Hi-C), and gene annotati…
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 9, 2026Jun 9, 2026

    • CompExonSpace

      Public
      This repository contains the code used to analyze the data presented in the manuscript "Specificity and exon target space of splicing modifying compounds”.
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Jun 8, 2026Jun 8, 2026

    • tinydenseR

      Public
      tinydenseR is a landmark-based platform for single cell data analysis that identifies differential cell states and features. Modeling samples as replicates, tin…
      R
      •
      Other
      •2•7•0•0•Updated May 27, 2026May 27, 2026

    • UNIQUE

      Public
      A Python library for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions.
      machine-learningcalibrationuncertainty-quantification
      machine-learningcalibrationuncertainty-quantification
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •9•51•0•1•Updated May 25, 2026May 25, 2026

    • moo-evaluation-framework

      Public
      A Python framework for evaluating and comparing multi-objective optimization (MOO) algorithms in molecular design and drug discovery.
      Python
      •
      MIT License
      •0•0•0•0•Updated May 11, 2026May 11, 2026

    • monitOS

      Public
      Monitoring overall survival in pivotal trials for indolent cancer
      monitoringsurvivalindolent
      monitoringsurvivalindolent
      R
      •
      Other
      •1•2•0•0•Updated Apr 15, 2026Apr 15, 2026

    • WATCH

      Public
      An R-repository to implement a double robust version of the WATCH workflow published in Sechidis et al. (2024)
      R
      •
      MIT License
      •2•4•0•0•Updated Mar 12, 2026Mar 12, 2026

    • pdiff

      Public
      generative text-to-imaging model for predicting cell phenotypic responses to compounds via high content imaging
      Python
      •
      MIT License
      •1•2•1•0•Updated Mar 11, 2026Mar 11, 2026

    • Pipeline_for_TES_AAV_LongReads

      Public
      This pipeline is designed for AAV integration site analysis using Target Enrichment Sequencing (TES) coupled with PacBio long-read sequencing. It enables the de…
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • attrib-path

      Public
      Parse a simplified JSONPath-like syntax
      TypeScript
      •
      Apache License 2.0
      •0•1•0•4•Updated Jan 24, 2026Jan 24, 2026

    • Novartis.github.io

      Public
      Public gallery of BR Open Source projects
      HTML
      •3•2•0•2•Updated Jan 19, 2026Jan 19, 2026

    • ChemScreener

      Public
      ChemScreener is an active learning pipeline for small-molecule screening. In each cycle, it trains an ensemble of multi-task Chemprop models, scores an unlabele…
      Python
      •
      MIT License
      •1•5•0•0•Updated Dec 19, 2025Dec 19, 2025

    • OncoBayes2

      Public
      Bayesian logistic regression with optional EX/NEX modeling enables flexible borrowing from historical or concurrent data. The safety model supports dose-escalat…
      R
      •
      GNU General Public License v3.0
      •3•4•0•1•Updated Dec 18, 2025Dec 18, 2025

    • synthetic-mris

      Public
      This project demonstrates how to train a model that can generate synthetic brain (T1w) MRI data. The work was presented as a poster at ICAART 2025. Our code tra…
      Python
      •
      Other
      •0•2•0•0•Updated Dec 16, 2025Dec 16, 2025

    • singleCellComic

      Public
      singeCellComic is an interactive Shiny application designed to teach the fundamental concepts of single-cell RNA sequencing (scRNA-seq) analysis through a fun, …
      R
      •
      MIT License
      •0•3•0•0•Updated Dec 9, 2025Dec 9, 2025

    • cellxgene-gateway

      Public
      Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple d…
      visualizationrna-seqdataviz
      visualizationrna-seqdatavizscrna-seqscientifictranscriptomicsh5ad
      Python
      •
      Apache License 2.0
      •41•69•13•4•Updated Dec 3, 2025Dec 3, 2025

    • subgroup_shrinkage

      Public
      Bayesian subgroup shrinkage estimation benchmark comparing various shrinkage models.
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Dec 2, 2025Dec 2, 2025

    • bamdd

      Public
      Applied modelling in drug development: flexible Bayesian regression modelling in Stan via brms
      clinicalbayesianstan
      clinicalbayesianstanbrms
      HTML
      •
      GNU General Public License v2.0
      •9•25•1•0•Updated Oct 21, 2025Oct 21, 2025

    • peakCombiner

      Public
      The fully R based tool peakCombiner is a user-friendly, transparent, modular and customizable package with the purpose to create a consensus peak file from geno…
      R
      •
      Other
      •4•6•0•0•Updated Sep 3, 2025Sep 3, 2025

    • xgx

      Public
      Exploratory Graphics for PKPD data
      HTML
      •
      MIT License
      •12•29•18•3•Updated Aug 30, 2025Aug 30, 2025

    • xgxr

      Public
      R package for supporting exploratory graphics at http://opensource.nibr.com/xgx
      R
      •
      Other
      •8•16•5•1•Updated Jul 12, 2025Jul 12, 2025
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