Novartis Open Source Initiative

tinydenseR is a landmark-based platform for single cell data analysis that identifies differential cell states and features. Modeling samples as replicates, tinydenseR enhances analytic efficiency and reproducibility while preserving the richness of single cell data.

testing repo for Nick

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.

A bslib toolkit for building modern, themeable dashboards in Shiny.

QM-ATLAS is a python package that orchestrates QM calculations. Based on thin wrappers of external software, more complex modules are built, exposing single calculation steps as well as multi-step workflows. The repository provides a flexible command-line interface that allows to define complex workflows in single configuration files.

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

N-nitrosamine Autonomous Carcinogenic Potency Categorization Approach Calculation Tool

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.

Deep survival analysis made easy

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