emcee v3 — Peer-reviewed • Rank 23.6 • Science 95%

emcee v3: A Python ensemble sampling toolkit for affine-invariant MCMC - Published in JOSS (2019)

exoplanet — Peer-reviewed • Rank 15.7 • Science 100%

exoplanet: Gradient-based probabilistic inference for exoplanet data & other astronomical time series - Published in JOSS (2021)

PyAutoFit — Peer-reviewed • Rank 15.2 • Science 100%

PyAutoFit: A Classy Probabilistic Programming Language for Model Composition and Fitting - Published in JOSS (2021)

AutoEmulate — Peer-reviewed • Rank 13.0 • Science 98%

AutoEmulate: A Python package for semi-automated emulation - Published in JOSS (2025)

flowMC — Peer-reviewed • Rank 15.8 • Science 95%

flowMC: Normalizing flow enhanced sampling package for probabilistic inference in JAX - Published in JOSS (2023)

VIP — Peer-reviewed • Rank 15.1 • Science 95%

VIP: A Python package for high-contrast imaging - Published in JOSS (2023)

fmcmc — Peer-reviewed • Rank 13.9 • Science 96%

fmcmc: A friendly MCMC framework - Published in JOSS (2019)

ParaMonte — Peer-reviewed • Rank 13.2 • Science 95%

ParaMonte: A high-performance serial/parallel Monte Carlo simulation library for C, C++, Fortran - Published in JOSS (2021)

pocoMC — Peer-reviewed • Rank 11.9 • Science 95%

pocoMC: A Python package for accelerated Bayesian inference in astronomy and cosmology - Published in JOSS (2022)

pygtc — Peer-reviewed • Rank 11.2 • Science 95%

pygtc: beautiful parameter covariance plots (aka. Giant Triangle Confusograms) - Published in JOSS (2016)

pymc • Rank 28.8 • Science 77%

Bayesian Modeling and Probabilistic Programming in Python

pymcmcstat — Peer-reviewed • Rank 10.5 • Science 95%

pymcmcstat: A Python Package for Bayesian Inference Using Delayed Rejection Adaptive Metropolis - Published in JOSS (2019)

Maelstrom — Peer-reviewed • Rank 7.0 • Science 95%

Maelstrom: A Python package for identifying companions to pulsating stars from their light travel time variations - Published in JOSS (2020)

PxMCMC — Peer-reviewed • Rank 6.4 • Science 95%

PxMCMC: A Python package for proximal Markov Chain Monte Carlo - Published in JOSS (2023)

stardate — Peer-reviewed • Rank 4.4 • Science 95%

stardate: Combining dating methods for better stellar ages - Published in JOSS (2019)

BAT • Rank 12.7 • Science 85%

A Bayesian Analysis Toolkit in Julia

Fitting a Gamma-Gompertz survival model to capture-recapture data collected on free-ranging animal populations — Peer-reviewed • Rank 1.4 • Science 95%

Fitting a Gamma-Gompertz survival model to capture-recapture data collected on free-ranging animal populations - Published in JOSS (2018)

mici • Rank 11.4 • Science 77%

Manifold Markov chain Monte Carlo methods in Python

nimble • Rank 20.9 • Science 59%

The base NIMBLE package for R

stochopy • Rank 12.4 • Science 67%

Python library for stochastic numerical optimization

Turing • Rank 19.4 • Science 59%

Bayesian inference with probabilistic programming.

getdist • Rank 16.9 • Science 59%

MCMC sample analysis, kernel densities, plotting, and GUI

pigeons.jl • Rank 11.4 • Science 64%

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

anesthetic — Peer-reviewed • Rank 16.2 • Science 59%

anesthetic: nested sampling visualisation - Published in JOSS (2019)

https://github.com/choderalab/openmmtools • Rank 13.1 • Science 59%

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

l2hmc-qcd • Rank 5.8 • Science 64%

Application of the L2HMC algorithm to simulations in lattice QCD.

storage-ring-gravitational-wave-observatory • Rank 0.7 • Science 67%

Simulating the detection of millihertz (mHz) gravitational waves (GWs) from astrophysical sources by a Storage Ring Gravitational-wave Observatory (SRGO).

https://github.com/pyro-ppl/numpyro • Rank 12.6 • Science 46%

Probabilistic programming with NumPy powered by JAX for autograd and JIT compilation to GPU/TPU/CPU.

starfish • Rank 7.2 • Science 51%

Tools for Flexible Spectroscopic Inference

walker • Rank 12.1 • Science 46%

Bayesian Generalized Linear Models with Time-Varying Coefficients

BayesianTools • Rank 19.7 • Science 33%

General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics

BAS • Rank 14.1 • Science 36%

BAS R package for Bayesian Model Averaging and Variable Selection

@stdlib/nlp-lda • Rank 5.5 • Science 44%

Latent Dirichlet Allocation via collapsed Gibbs sampling.

mc3 • Rank 11.6 • Science 36%

Python MCMC Sampler

https://github.com/4ment/physher • Rank 3.5 • Science 39%

A multi-algorithmic framework for phylogenetic inference

bfw • Rank 9.4 • Science 33%

Framework for conducting Bayesian analyses

https://github.com/poissonconsulting/mcmcr • Rank 15.9 • Science 26%

An R package to manipulate MCMC samples

https://github.com/cbg-ethz/scicone • Rank 5.2 • Science 36%

Single-cell copy number calling and event history reconstruction.

shinybrms • Rank 12.3 • Science 26%

An R package providing a GUI ('shiny' app) for the R package 'brms'.

https://github.com/aesara-devs/aehmc • Rank 9.6 • Science 26%

An HMC/NUTS implementation in Aesara

tweetopic • Rank 9.4 • Science 26%

Blazing fast topic modelling for short texts.

mcmcderive • Rank 8.9 • Science 26%

Calculate derived parameters from MCMC samples

https://github.com/cbg-ethz/bnpc • Rank 4.7 • Science 26%

Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates

https://github.com/anthofflab/robustadaptivemetropolissampler.jl • Rank 7.0 • Science 23%

A Julia implementation of the RAM algorithm (Vihola, 2012)

remiod • Rank 6.4 • Science 23%

R package for controlled multiple imputation of ordinal or binary responses with missing data in clinical study

ggmcmc • Rank 19.0 • Science 10%

Graphical tools for analyzing Markov Chain Monte Carlo simulations from Bayesian inference

https://github.com/4ment/flc • Rank 2.9 • Science 26%

Local clock model using relaxed and strict clocks

bvartools • Rank 15.0 • Science 13%

Functions for Bayesian inference of vector autoregressive and vector error correction models

https://github.com/4ment/skyplotr • Rank 0.7 • Science 26%

https://github.com/bisaloo/mcmcensemble • Rank 13.6 • Science 13%

R Package Providing Ensemble Sampler for Affine-Invariant MCMC

AdMit • Rank 11.4 • Science 13%

Adaptive Mixture of Student-t distributions

https://github.com/axsk/gync.jl • Rank 2.3 • Science 13%

Bayesian inference for the GynCycle model

https://github.com/ahasverus/samplesim • Rank 0.7 • Science 13%

:package: Estimating sample size effects in stable isotope mixing solutions

https://github.com/isms/mcmc-rs • Rank 2.5 • Science 10%

A Rust library implementing various MCMC diagnostics and utilities, such as Gelman Rubin potential scale reduction factor (R hat), effective sample size, chain splitting, and others.

LinFit • Rank 0.0 • Science 10%

Linear regression with MCMC (under test)

manifold_lifting • Science 67%

Accompanying code for 'Manifold lifting: scaling MCMC to the vanishing noise regime'

simtost • Science 26%

SimTOST is an R package designed to facilitate the sample size estimation for bioequivalence studies using a simulation-based approach.

rmcmc • Science 57%

Robust Markov chain Monte Carlo methods in R

alaamee • Science 67%

Autologistic Actor Attribute Model (ALAAM) parameter estimation, simulation, and goodness-of-fit

rbvfit • Science 49%

A Bayesian Voigt profile fitter. Optimized for absorption line analysis.

https://github.com/chalk-lab/mcmctempering.jl • Science 26%

Implementations of parallel tempering algorithms to augment samplers with tempering capabilities

posteriorplots.jl • Science 41%

Graphical tools for Bayesian inference and posterior predictive checks

polymer-stats • Science 67%

Computational statistical mechanics of field-responsive polymer chains

https://github.com/baggepinnen/turing2montecarlomeasurements.jl • Science 23%

Interface between Turing.jl and MonteCarloMeasurements.jl

https://github.com/compevol/sampled-ancestors • Science 39%

This BEAST2 package provides MCMC proposals and post-processing tools for sampling trees containing sampled ancestors

ssme • Science 54%

a c++ library for the estimation of state-space models

bnpmixcluster • Science 13%

Model-based clustering with mixed scale variables

https://github.com/compevol/beast2 • Science 36%

Bayesian Evolutionary Analysis by Sampling Trees

speclet • Science 26%

A Bayesian hierarchical model to discover tissue-specific cancer driver genes and synthetic lethal interactions from CRISPR/Cas9 LoF screens.

https://github.com/fgittins/montepython • Science 26%

A Markov chain-Monte Carlo sampler.

estimnetdirected • Science 67%

Equilibrium Expectation for ERGM parameter estimation for large networks

https://github.com/bluebrain/emodel-generalisation • Science 62%

Generalisation of electrical models of neurons with MCMC

https://github.com/bonstats/smcdar • Science 23%

Data and code to accompany paper "Accelerating sequential Monte Carlo with surrogate likelihoods"

manifold-mcmc-for-diffusions • Science 54%

Code accompanying the paper 'Manifold MCMC methods for Bayesian inference in a wide class of diffusion models'