Projects in Awesome Lists by Novartis
A curated list of projects in awesome lists by Novartis .
https://github.com/Novartis/torchsurv
Deep survival analysis made easy
deep-learning pytorch survival-analysis
Last synced: 28 Sep 2025
https://github.com/novartis/tidymodules
An Object-Oriented approach to Shiny modules
communication inheritance oop r shiny shiny-modules tidy-operators
Last synced: 03 Nov 2025
https://github.com/Novartis/tidymodules
An Object-Oriented approach to Shiny modules
communication inheritance oop r shiny shiny-modules tidy-operators
Last synced: 08 May 2025
https://github.com/novartis/torchsurv
Deep survival analysis made easy
deep-learning pytorch survival-analysis
Last synced: 26 Jan 2026
https://github.com/novartis/peax
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
autoencoder data-visualization deep-learning epigenomics interactive-machine-learning pattern-search sequential-data
Last synced: 21 Jul 2025
https://github.com/Novartis/peax
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
autoencoder data-visualization deep-learning epigenomics interactive-machine-learning pattern-search sequential-data
Last synced: 07 May 2025
https://github.com/novartis/cellxgene-gateway
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
dataviz h5ad rna-seq scientific scrna-seq transcriptomics visualization
Last synced: 21 Jul 2025
https://github.com/Novartis/cellxgene-gateway
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
dataviz h5ad rna-seq scientific scrna-seq transcriptomics visualization
Last synced: 28 Sep 2025
https://github.com/novartis/scar
scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
cite-seq crispr-screen denoising-algorithm generative-model machine-learning probabilistic-graphical-models pytorch single-cell-rna-seq variational-autoencoder
Last synced: 21 Jul 2025
https://github.com/Novartis/scar
scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
cite-seq crispr-screen denoising-algorithm generative-model machine-learning probabilistic-graphical-models pytorch single-cell-rna-seq variational-autoencoder
Last synced: 28 Sep 2025
https://github.com/novartis/shinyvalidator
Audit your Shiny apps at each commit. Multiple levels of testings are offered: startup and crash tests, performance tests (load test and global code profiling), reactivity audit as well as output tests. All results are gathered in an HTML report uploaded and available to everyone on any CI/CD plaform or RStudio Connect
audit headless profiling r shiny shinyloadtest shinytest2
Last synced: 21 Jul 2025
https://github.com/Novartis/shinyValidator
Audit your Shiny apps at each commit. Multiple levels of testings are offered: startup and crash tests, performance tests (load test and global code profiling), reactivity audit as well as output tests. All results are gathered in an HTML report uploaded and available to everyone on any CI/CD plaform or RStudio Connect
audit headless profiling r shiny shinyloadtest shinytest2
Last synced: 06 May 2025
https://github.com/novartis/ontobrowser
OntoBrowser is a web-based application for managing ontologies
Last synced: 21 Jul 2025
https://github.com/Novartis/ontobrowser
OntoBrowser is a web-based application for managing ontologies
Last synced: 28 Sep 2025
https://github.com/novartis/unique
A Python library for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions.
calibration machine-learning uncertainty-quantification
Last synced: 21 Jul 2025
https://github.com/novartis/pqsar
Massively multitask stacked model for predicting activity of thousands of biological assays
Last synced: 21 Jul 2025
https://github.com/Novartis/pisces
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
bioinformatics bioinformatics-pipeline rnaseq rnaseq-pipeline salmon transcriptomics
Last synced: 28 Sep 2025
https://github.com/novartis/pqsar2cpd
pqsar2cpd is a deep learning algorithm for translation of activity profiles into novel molecules.
Last synced: 21 Jul 2025
https://github.com/novartis/pisces
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
bioinformatics bioinformatics-pipeline rnaseq rnaseq-pipeline salmon transcriptomics
Last synced: 21 Jul 2025
https://github.com/Novartis/yap
High throughput, pain-free big data pipelines.
Last synced: 28 Sep 2025
https://github.com/novartis/yap
High throughput, pain-free big data pipelines.
Last synced: 21 Jul 2025
https://github.com/Novartis/pQSAR
Massively multitask stacked model for predicting activity of thousands of biological assays
Last synced: 28 Sep 2025
https://github.com/Novartis/JAEGER
JAEGER is a deep generative approach for small-molecule design
Last synced: 28 Sep 2025
https://github.com/novartis/chembiomultimodalautoencoders
a package for streamlined multidomain data integration and translation based on cross-modal autoencoders architectures
Last synced: 21 Jul 2025
https://github.com/Novartis/ChemBioMultimodalAutoencoders
a package for streamlined multidomain data integration and translation based on cross-modal autoencoders architectures
Last synced: 28 Sep 2025
https://github.com/Novartis/pqsar2cpd
pqsar2cpd is a deep learning algorithm for translation of activity profiles into novel molecules.
Last synced: 28 Sep 2025
https://github.com/novartis/easytrackhubs
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.
Last synced: 05 Feb 2026
https://github.com/Novartis/easyTrackHubs
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.
Last synced: 28 Sep 2025
https://github.com/novartis/jaeger
JAEGER is a deep generative approach for small-molecule design
Last synced: 21 Jul 2025
https://github.com/Novartis/Causal-inference-in-RCTs
This repository contains code examples for several methods in a Causal Inference in RCTs short course.
Last synced: 28 Sep 2025
https://github.com/novartis/causal-inference-in-rcts
This repository contains code examples for several methods in a Causal Inference in RCTs short course.
Last synced: 21 Jul 2025
https://github.com/novartis/bamdd
Applied modelling in drug development: flexible Bayesian regression modelling in Stan via brms
Last synced: 07 Feb 2026
https://github.com/novartis/rbest
Tool-set to support Bayesian evidence synthesis in R
bayesian clinical historical-data meta-analysis
Last synced: 21 Jul 2025
https://github.com/novartis/drug-seq
DRUG (Digital RNA with pertUrbation of Genes)-seq data analysis pipeline
Last synced: 21 Jul 2025
https://github.com/Novartis/DRUG-seq
DRUG (Digital RNA with pertUrbation of Genes)-seq data analysis pipeline
Last synced: 28 Sep 2025
https://github.com/novartis/patprofile
Standard patient profile for shiny apps
Last synced: 21 Jul 2025
https://github.com/Novartis/patprofile
Standard patient profile for shiny apps
Last synced: 28 Sep 2025
https://github.com/novartis/moabox
A repository of compound-target annotations in support of Systematic Chemogenetic Library Assembly
Last synced: 06 Feb 2026
https://github.com/novartis/gridvar
GridVar is a jQuery plugin that visualizes multi-dimensional datasets as layers organized in a row-column format.
Last synced: 21 Jul 2025
https://github.com/novartis/railroadtracks
Railroadtracks is a Python package to handle connected computation steps for DNA and RNA Seq.
Last synced: 21 Jul 2025
https://github.com/novartis/xgxr
R package for supporting exploratory graphics at http://opensource.nibr.com/xgx
Last synced: 21 Jul 2025
https://github.com/novartis/jenkins-lsci
Jenkins for Life Science Continuous Integration
Last synced: 21 Jul 2025
https://github.com/novartis/umm-discovery
UMM-Discovery is a fully unsupervised deep learning method to cluster cellular images with similar phenotypes together, solely based on the intensity values.
deep-learning moa unsupervised
Last synced: 15 Feb 2026
https://github.com/novartis/div_rank
This code allows is for diversity picking across multiple different, and potentially overlapping chemical compound classes, while at the same time optimizing a property score. This algorithm has been used in the re-design of the Novartis screening deck as described in https://dx.doi.org/10.1021/acs.jmedchem.0c01332
Last synced: 21 Jul 2025
https://github.com/novartis/eqp-cluster
Unix-based RNA-seq quantification pipeline
Last synced: 21 Jul 2025
https://github.com/novartis/scrnaseq_workflow_benchmark
Workflow for the analysis fo single-cell RNASeq data using R/bioconductor
Last synced: 21 Jul 2025
https://github.com/novartis/habitat
"Where files live" - Simple object management system using AWS S3 and Elasticsearch Service to manage objects and their metadata
Last synced: 21 Jul 2025
https://github.com/Novartis/habitat
"Where files live" - Simple object management system using AWS S3 and Elasticsearch Service to manage objects and their metadata
Last synced: 29 Jul 2025
https://github.com/novartis/hpath
An ontology of histopathological morphologies
Last synced: 05 Feb 2026
https://github.com/novartis/subpat
{subpat} is a collection of modules to create subpopulations and subgroups from clinical trial data
Last synced: 21 Jul 2025
https://github.com/novartis/toolscore
Script and example data for "Evidence-Based and Quantitative Prioritization of Tool Compounds in Phenotypic Drug Discovery"
Last synced: 21 Jul 2025
https://github.com/novartis/ndsris_in_silico_tool
N-nitrosamine Autonomous Carcinogenic Potency Categorization Approach Calculation Tool
Last synced: 31 Jul 2025
https://github.com/novartis/spd
A novel preclinical secondary pharmacology resource illuminates target-adverse drug reaction associations of marketed drugs
Last synced: 21 Jul 2025
https://github.com/novartis/dms-pipeline
Snakemake pipeline for quantification of deep mutational scanning (DMS) data from overlapping paired-end reads in fastq files from amplicon sequencing
Last synced: 21 Jul 2025
https://github.com/novartis/peakcombiner
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.
Last synced: 21 Jul 2025
https://github.com/novartis/cellsius
CellSIUS: Cell Subtype Identification from Upregulated gene Sets
Last synced: 21 Jul 2025
https://github.com/novartis/chraw
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.
Last synced: 08 Aug 2025
https://github.com/novartis/project-mona-lisa
Project Mona Lisa (PML): Machine-learning Assisted Diagramming Platform
Last synced: 21 Jul 2025
https://github.com/novartis/verifyr
A package to hold R functions for comparing different version of clinical trial TLFs
Last synced: 21 Jul 2025
https://github.com/novartis/trawling
Description: Build TRAWLING: a Transcriptome Reference AWare of spLicING events
Last synced: 21 Jul 2025
https://github.com/novartis/tat
Transcriptomics-to-Activity Transformer (TAT) is a deep learning model to predict compound bioactivity in a dose-response assay using compound-induced transcriptomic profiles over concentration.
Last synced: 21 Jul 2025
https://github.com/novartis/greychemicalmatter
A pipeline to identify bioactive small molecules with likely novel modes of actions and dynamic SAR from historic cell-HTS profiles, with an example application and hitlist from PubChem data
Last synced: 21 Jul 2025
https://github.com/novartis/monitos
Monitoring overall survival in pivotal trials for indolent cancer
Last synced: 21 Jul 2025
https://github.com/novartis/mvac50
AC50 potencies from multivariate assay readouts like gene signatures
Last synced: 21 Jul 2025
https://github.com/novartis/novartis.github.io
Public gallery of NIBR Open Source projects
Last synced: 07 Feb 2026
https://github.com/novartis/solid-tumor-chip
Clonal hematopoiesis detection in cancer patients using cell free DNA sequencing
Last synced: 07 Feb 2026
https://github.com/novartis/watmd
Water tool for molecular dynamics that calculates solvation fields for interaction between water and non-solvant molecules
Last synced: 06 Feb 2026
https://github.com/novartis/cell-reports-d-21-02389r1
Analysis scripts and processed data for CELL-REPORTS-D-21-02389R3
Last synced: 21 Jul 2025
https://github.com/novartis/eqp-qm
Unix based RNA-seq quantification module
Last synced: 21 Jul 2025
https://github.com/novartis/rdocx
Create and edit reporting documents using R
Last synced: 21 Jul 2025
https://github.com/novartis/dpasurv
An R-package for performing dynamic path analysis on survival data with estimation of the corresponding direct, indirect, and total effects.
Last synced: 02 Sep 2025
https://github.com/novartis/profile-qsar
Massively multitask stacked model for predicting activity of thousands of biological assays
Last synced: 21 Jul 2025
https://github.com/novartis/cu-catalyzed-ligands-design
By establishing machine learning (ML) models, the design of ligands and optimization of reaction conditions were effectively facilitated
Last synced: 21 Jul 2025
https://github.com/novartis/mueller_et_al_2018
Processed data relating to Continuous monitoring of patient mobility for 18 months using inertial sensors following traumatic knee injury: a case study Mueller A., Hoefling H., Nuritdinow T., et al. Paper: http://doi.org/10.1159/000490919 Raw data: http://doi.org/10.5281/zenodo.1443190
Last synced: 07 Feb 2026
https://github.com/novartis/knockofftools
An R-package containing a suite of knockoffs functions and methods from existing R-packages and the knockoffs literature. Some of the R functions are novel implementations of recent methods.
Last synced: 21 Jul 2025
https://github.com/novartis/beyond-pk-score
Prediction of Small-Molecule Developability Using Large-Scale In Silico ADMET Models
Last synced: 21 Jul 2025
https://github.com/novartis/tf_prioritization_benchmark_gb2023
Code to reproduce the paper figures from TF prioritization tool outputs.
Last synced: 16 Feb 2026
https://github.com/novartis/chemicalseriesreconstruction
25 Years of Small-Molecule Optimization at Novartis: A Retrospective Analysis of Chemical Series Evolution
Last synced: 21 Jul 2025
https://github.com/novartis/frpipe
FRPipe: A 19F NMR data analysis pipeline
Last synced: 21 Jul 2025
https://github.com/novartis/xgx_v1
Version 1 of xgx. This version does not require the xgxr package
Last synced: 10 Feb 2026
https://github.com/novartis/jenkins-lsci-jobs
Jenkins jobs that support a variety of life science applications (data management, data transformations, analysis, computational workflows etc.)
Last synced: 21 Jul 2025
https://github.com/novartis/monolixident
Monolix identifiability assessment R package for generating likelihood profiles (LLPs) and likelihood waterfalls (LLW) using Batchtools for parallelization.
Last synced: 04 Feb 2026
https://github.com/novartis/watch
An R-repository to implement a double robust version of the WATCH workflow published in Sechidis et al. (2024)
Last synced: 21 Jul 2025
https://github.com/novartis/cnv-analysis
Confluent and overlapping cells are difficult to quantify in low power images. This MatLab code allows a user to analyze the pixel intensity (integrated density) over a region of interest (ROI) in low power images as a surrogate for cell number. This code was optimized for use in our Choroidal Neovascularization model, and allows for the analysis of three ROIs per image. Both the intensity gate and the radius of ROI's can be changed to meet the needs of the project.
Last synced: 08 Feb 2026
https://github.com/novartis/rescalestx
This is a package for rescaling coordinates for Visium 10x transcriptomics datasets. This enables the highest resolution (or an arbitrary resolution) of microscopy image to be used for STx analysis, which enables advanced image processing and machine-learning using image features and coordinates of spatial transcriptomics datasets
Last synced: 07 Oct 2025