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    116 repositories

    • bslibdash

      Public
      A bslib toolkit for building modern, themeable dashboards in Shiny.
      R
      •
      Other
      •0•1•0•0•Updated Oct 2, 2026Oct 2, 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•31•10•2•Updated Oct 1, 2026Oct 1, 2026

    • qm-atlas

      Public
      QM-ATLAS is a python package that orchestrates QM calculations. Based on thin wrappers of external software, more complex modules are built, exposing single cal…
      Python
      •
      MIT License
      •0•13•0•0•Updated Sep 29, 2026Sep 29, 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•26•0•0•Updated Sep 18, 2026Sep 18, 2026

    • pankrasi_ct26_scrnaseq_analysis

      Public
      Rscripts used to analyze single cell RNAseq data for "A Potent Macrocyclic pan-KRAS Inhibitor Drives Broad Antitumor Activity and Immune Remodeling" manuscript.
      MIT License
      •0•0•0•0•Updated Sep 17, 2026Sep 17, 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
      •3•7•0•0•Updated Sep 15, 2026Sep 15, 2026

    • osi-push-test

      Public
      testing repo for Nick
      0•0•0•0•Updated Sep 15, 2026Sep 15, 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 Sep 15, 2026Sep 15, 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•59•0•1•Updated Sep 11, 2026Sep 11, 2026

    • NDSRIs_in_silico_tool

      Public
      N-nitrosamine Autonomous Carcinogenic Potency Categorization Approach Calculation Tool
      Jupyter Notebook
      •
      Apache License 2.0
      •3•11•1•0•Updated Sep 7, 2026Sep 7, 2026

    • chraw

      Public
      The package analyzes chromatin and multi-omic experiments. It extends the MultiAssayExperiment object and builds a ChrawExperiment object from ENCODE’s output. …
      R
      •
      Other
      •2•6•1•0•Updated Sep 2, 2026Sep 2, 2026

    • torchsurv

      Public
      Deep survival analysis made easy
      deep-learningpytorchsurvival-analysis
      deep-learningpytorchsurvival-analysis
      Python
      •
      MIT License
      •17•216•5•3•Updated Aug 27, 2026Aug 27, 2026

    • 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•26•0•0•Updated Aug 24, 2026Aug 24, 2026

    • xgx

      Public
      Exploratory Graphics for PKPD data
      R
      •
      MIT License
      •13•30•18•3•Updated Aug 18, 2026Aug 18, 2026

    • caMPO

      Public
      Implementation of caMPO (Correlation-aware Multiparameter Optimization), a method for deriving data-driven non-negative MPO weights from property correlation st…
      MIT License
      •0•2•0•0•Updated Aug 18, 2026Aug 18, 2026

    • admin

      Public
      Go here for requests and support
      0•0•1•0•Updated Aug 17, 2026Aug 17, 2026

    • orthoMTL

      Public
      R
      •0•1•0•0•Updated Aug 7, 2026Aug 7, 2026

    • 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 Aug 4, 2026Aug 4, 2026

    • frequent-hitters

      Public
      Data pre-processing and chemprop model for frequent hitter prediction
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 4, 2026Aug 4, 2026

    • xgxr

      Public
      R package for supporting exploratory graphics at http://opensource.nibr.com/xgx
      R
      •
      Other
      •8•16•3•1•Updated Aug 3, 2026Aug 3, 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
      •1•2•0•0•Updated Jul 30, 2026Jul 30, 2026

    • AVIDbase

      Public
      Computational pipeline for the preparation of the AVIDbase dataset of nanobody-antigen crystal structures from the PDB.
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 29, 2026Jul 29, 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
      •1•28•0•0•Updated Jul 6, 2026Jul 6, 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•2•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•1•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

    • 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
      •3•4•0•1•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•3•1•0•Updated Mar 11, 2026Mar 11, 2026
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