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

Tool-set to support Bayesian evidence synthesis in R

synadam is an R package that generates synthetic ADaM clinical trial datasets from real data using a glimpse-then-simulate approach. It preserves statistical properties and data structure while removing patient identifiers, enabling safe data sharing for pharmaceutical research and regulatory collaboration.

Deep survival analysis made easy

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

Computational pipeline for the preparation of the AVIDbase dataset of nanobody-antigen crystal structures from the PDB.

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.

NODE is an R package for identifying transcription factor (TF) target genes by integrating TF binding sites, 3D chromatin interactions (Hi-C), and gene annotations. It builds a genomic graph to find regulatory paths from distal elements to gene promoters.

This repository contains the code used to analyze the data presented in the manuscript "Specificity and exon target space of splicing modifying compounds”.