Deep survival analysis made easy

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

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.

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.

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

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.

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.

Exploratory Graphics for PKPD data

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

Parse a simplified JSONPath-like syntax