MCMC algorithms for staged trees

Bayesian Evolutionary Analysis Sampling Trees

Dampa: Diversity Aware Metagenomic Panel Assignment

R package for gRaphical independence networks (Bayesian networks)

Transcriptional Inference using Gene Expression and Regulatory data

Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.

Repo for the R package coloc

Targeted inference (R package) https://kkholst.github.io/targeted/

Vivarium simulation backend

Yet another redundant workflow engine

An R package for stratified staged probability event trees

Julia package for performing rigorous arithmetic of Imprecise Probabilities with fuzzy numbers

An R package for stratified staged probability event trees

Sampling from intractable distributions, with support for distributed and parallel methods

bnmonitor R package

PennyLane is an open-source quantum software platform for quantum computing, quantum machine learning, and quantum chemistry. Create meaningful quantum algorithms, from inspiration to implementation.

AlphaFold 3 inference pipeline.

A framework with a reduced state space to train the Arrhenius DNA kinetic model

chain-event graph for R. This package implements the theory of CEG. Generate and plot CEG objects from manual input or from formatted data.

Python Combinatorial Optimisation Platform

Implementation for paper: Learning from Uncertain Data: From Possible Worlds to Possible Models.

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples.

time course regulatory analysis from paired gene expression and chromatin accessibility time course data

Symphony algorithm for inference of cell type specific gene regulatory networks from scRNA-seq and ATAC-seq

A course on imprecise probabilistic machine learning

Qiskit is an open-source SDK for working with quantum computers at the level of extended quantum circuits, operators, and primitives.

Snowflurry is an open source Julia-based software library for implementing quantum circuits, and then running them on quantum computers and quantum simulators. The project is sponsored by Anyon Sys…