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Novartis's repositories

tidymodules

An Object-Oriented approach to Shiny modules

Language:RNOASSERTION144 11 32

torchsurv

Deep survival analysis made easy

Language:PythonMIT118 7 55

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.

Language:PythonApache-2.061 11 64

scar

scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics

Language:Python51 7 20

UNIQUE

A Python library for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions.

Language:PythonBSD-3-Clause31 6 2

pisces

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Language:PythonApache-2.030 1 22

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.

Language:HTMLGPL-3.028 50

DRUG-seq

DRUG (Digital RNA with pertUrbation of Genes)-seq data analysis pipeline

Language:RMIT26 70

Causal-inference-in-RCTs

This repository contains code examples for several methods in a Causal Inference in RCTs short course.

Language:RMIT25 40

RBesT

Tool-set to support Bayesian evidence synthesis in R

Language:RGPL-3.023 3 8

bamdd

Applied modelling in drug development: flexible Bayesian regression modelling in Stan via brms

Language:HTMLGPL-2.020 5 9

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.

Language:RMIT5 20

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.

Language:RNOASSERTION5 30

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.

Language:PythonApache-2.05 30

verifyr

A package to hold R functions for comparing different version of clinical trial TLFs

Language:Rich Text FormatMIT5 1 8

DeepCt

Predicting pharmacokinetic compartmental models and concentration-time curves from chemical structure using deep learning

Language:Jupyter NotebookBSD-3-Clause3 2 1

rdocx

Create and edit reporting documents using R

Language:RMIT3 20

monitOS

Monitoring overall survival in pivotal trials for indolent cancer

Language:RMIT2 20

ChemicalSeriesReconstruction

25 Years of Small-Molecule Optimization at Novartis: A Retrospective Analysis of Chemical Series Evolution

Language:PythonBSD-3-Clause1 10

Cu-Catalyzed-Ligands-Design

By establishing machine learning (ML) models, the design of ligands and optimization of reaction conditions were effectively facilitated

Language:Jupyter NotebookMIT1 20

dpasurv

An R-package for performing dynamic path analysis on survival data with estimation of the corresponding direct, indirect, and total effects.

Language:RNOASSERTION1 2 2

dWIZGenomics

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"

Language:RGPL-3.01 20

knockoffs-cpt2024paper-simulations

An R-repository to run simulation studies as in the paper 'All that glitters is not gold: Type-I error controlled variable selection from clinical trial data' by Zimmermann et al. (2024)

Language:RMIT1 20

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.

Language:RMIT1 3 1

risk_assessments

Repository collecting risk assessment data on the packages installed on our Statistical Computing Environment at Novartis.

MIT1 10

TF_Prioritization_Benchmark_GB2023

Code to reproduce the paper figures from TF prioritization tool outputs.

MIT020

beyond-PK-score

Prediction of Small-Molecule Developability Using Large-Scale In Silico ADMET Models

Language:Jupyter NotebookBSD-3-Clause010

px_tmt_daa

Differential abundance analysis of proteomics (TMT) data

MIT020

scOTGM

This is the official codebase for "sc-OTGM: Single-Cell Perturbation Modeling by Solving Optimal Mass Transport on the Manifold of Gaussian Mixtures"

Language:Jupyter NotebookGPL-3.0010

WATCH

An R-repository to implement a double robust version of the WATCH workflow published in Sechidis et al. (2024)

Language:RMIT030