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    99 repositories

    • tinydenseR

      Public
      tinydenseR is a landmark-based platform for single cell data analysis that identifies differentially abundant cell types and differentially expressed features, including subtle within-cluster state changes. Modeling samples as replicates, tinydenseR enhances analytic efficiency and reproducibility while preserving the richness of single cell data
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • torchsurv

      Public
      Deep survival analysis made easy
      deep-learningpytorchsurvival-analysis
      Python
      •
      MIT License
      •14•161•6•0•Updated Oct 31, 2025Oct 31, 2025

    • bamdd

      Public
      Applied modelling in drug development: flexible Bayesian regression modelling in Stan via brms
      clinicalbayesianstanbrms
      HTML
      •
      GNU General Public License v2.0
      •6•24•0•0•Updated Oct 21, 2025Oct 21, 2025

    • slc-localization

      Public
      The codebase created to support the application of artificial intelligence for predicting the subcellular localization of solute carrier transporter (SLC) proteins. We developed an iterative method that harmonizes human annotations with AI-based model outputs.
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 20, 2025Oct 20, 2025

    • OncoBayes2

      Public
      Bayesian logistic regression with optional EX/NEX modeling enables flexible borrowing from historical or concurrent data. The safety model supports dose-escalation in adaptive Phase I oncology trials with multiple drugs. See Neuenschwander et al. (2008, 2016) for methodology.
      R
      •
      GNU General Public License v3.0
      •1•1•0•1•Updated Oct 17, 2025Oct 17, 2025

    • 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 detection of integration site breakpoints and provides information on the structure of the integrated AAV vector genome to support the safety assessment of AAV-based gene therapies.
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 12, 2025Sep 12, 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 genomic input regions. The aim is to allow even novice R users to create good quality combined peak sets to be used as the starting point for most downstream differential analyses.
      R
      •
      Other
      •4•5•0•0•Updated Sep 3, 2025Sep 3, 2025

    • xgx

      Public
      Exploratory Graphics for PKPD data
      HTML
      •
      MIT License
      •11•27•18•3•Updated Aug 30, 2025Aug 30, 2025

    • 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•26•0•0•Updated Aug 1, 2025Aug 1, 2025

    • attrib-path

      Public
      Parse a simplified JSONPath-like syntax
      TypeScript
      •
      Apache License 2.0
      •0•1•0•1•Updated Jul 22, 2025Jul 22, 2025

    • monitOS

      Public
      Monitoring overall survival in pivotal trials for indolent cancer
      R
      •
      Other
      •1•2•0•0•Updated Jul 21, 2025Jul 21, 2025

    • xgxr

      Public
      R package for supporting exploratory graphics at http://opensource.nibr.com/xgx
      R
      •
      Other
      •8•13•4•1•Updated Jul 12, 2025Jul 12, 2025

    • pisces

      Public
      PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
      bioinformaticsbioinformatics-pipelinernaseqtranscriptomicssalmonrnaseq-pipeline
      Python
      •
      Apache License 2.0
      •3•30•10•2•Updated Jun 17, 2025Jun 17, 2025

    • RBesT

      Public
      Tool-set to support Bayesian evidence synthesis in R
      clinicalbayesianmeta-analysishistorical-data
      R
      •
      GNU General Public License v3.0
      •2•24•1•0•Updated May 13, 2025May 13, 2025

    • DRUG-seq

      Public
      DRUG (Digital RNA with pertUrbation of Genes)-seq data analysis pipeline
      R
      •
      MIT License
      •12•33•0•0•Updated Mar 19, 2025Mar 19, 2025

    • rdocx

      Public
      Create and edit reporting documents using R
      R
      •
      MIT License
      •1•5•0•0•Updated Nov 19, 2024Nov 19, 2024

    • risk_assessments

      Public
      Repository collecting risk assessment data on the packages installed on our Statistical Computing Environment at Novartis.
      MIT License
      •0•1•0•0•Updated Oct 8, 2024Oct 8, 2024

    • UNIQUE

      Public
      A Python library for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions.
      machine-learningcalibrationuncertainty-quantification
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•39•0•0•Updated Oct 4, 2024Oct 4, 2024

    • chraw

      Public
      The package analyzes chromatin and multi-omic experiments. It extends the MultiAssayExperiment object and builds a ChrawExperiment object from ENCODE’s output. It performs QC plotting, identifies differential events and other functionalities. More details in package vignettes.
      R
      •
      MIT License
      •2•5•0•0•Updated Sep 10, 2024Sep 10, 2024

    • beyond-PK-score

      Public
      Prediction of Small-Molecule Developability Using Large-Scale In Silico ADMET Models
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•0•0•Updated Sep 8, 2024Sep 8, 2024

    • ChemicalSeriesReconstruction

      Public
      25 Years of Small-Molecule Optimization at Novartis: A Retrospective Analysis of Chemical Series Evolution
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Sep 8, 2024Sep 8, 2024

    • tidymodules

      Public
      An Object-Oriented approach to Shiny modules
      rcommunicationshinyoopinheritanceshiny-modulestidy-operators
      R
      •
      Other
      •12•146•25•0•Updated Sep 5, 2024Sep 5, 2024

    • dpasurv

      Public
      An R-package for performing dynamic path analysis on survival data with estimation of the corresponding direct, indirect, and total effects.
      R
      •
      Other
      •0•2•0•0•Updated Aug 27, 2024Aug 27, 2024

    • DeepCt

      Public
      Predicting pharmacokinetic compartmental models and concentration-time curves from chemical structure using deep learning
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•1•0•Updated Aug 26, 2024Aug 26, 2024

    • scar

      Public
      scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
      machine-learningpytorchgenerative-modelprobabilistic-graphical-modelsvariational-autoencodersingle-cell-rna-seqdenoising-algorithmcite-seqcrispr-screen
      Python
      •5•55•4•0•Updated Aug 17, 2024Aug 17, 2024

    • Cu-Catalyzed-Ligands-Design

      Public
      By establishing machine learning (ML) models, the design of ligands and optimization of reaction conditions were effectively facilitated
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jun 27, 2024Jun 27, 2024

    • scOTGM

      Public
      This is the official codebase for "sc-OTGM: Single-Cell Perturbation Modeling by Solving Optimal Mass Transport on the Manifold of Gaussian Mixtures"
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 17, 2024May 17, 2024

    • WATCH

      Public
      An R-repository to implement a double robust version of the WATCH workflow published in Sechidis et al. (2024)
      R
      •
      MIT License
      •0•1•0•0•Updated May 17, 2024May 17, 2024

    • dWIZGenomics

      Public
      Provides the code used to reproduce the figures containing the genomic data for the publication "A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction"
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 2, 2024May 2, 2024

    • easyTrackHubs

      Public
      This package provides a function to reformat lists of genome coverage files, such as bigWig of bam files, into the directory structure of a UCSC Track Hub ready to be visualized in the genome browser. For details about it's use, please have a look at the vignette of the package.
      HTML
      •
      GNU General Public License v3.0
      •0•28•0•0•Updated Apr 29, 2024Apr 29, 2024