303 Open source projects that are alternatives of or similar to SCICoNE

A statistical toolbox for diffusion processes and stochastic differential equations. Named after the Brownian Bridge.

Blang's software development kit

The base NIMBLE package for R

Bayesian Deep Learning with Stochastic Gradient MCMC Methods

Pytorch implementations of Bayes By Backprop, MC Dropout, SGLD, the Local Reparametrization Trick, KF-Laplace, SG-HMC and more

Collection of Monte Carlo (MC) and Markov Chain Monte Carlo (MCMC) algorithms applied on simple examples.

Bayesian Data Analysis demos for R

Bayesian inference with probabilistic programming.

Full Bayesian Inference for Hidden Markov Models

RStan, the R interface to Stan

A common framework for implementing and using log densities for inference.

GPstuff - Gaussian process models for Bayesian analysis

Bayesian Data Analysis demos for Python

Doing Bayesian Data Analysis, 2nd Edition (Kruschke, 2015): Python/PyMC3 code

Multi-core BUGS for fast Bayesian inference of large hierarchical models

Sequential Monte Carlo algorithm for approximation of posterior distributions.

Nested Sampling post-processing and plotting

A Bayesian Analysis Toolkit in Julia

A web interface for exploring PyMC3 traces

Examples for Bayesian inference using DynamicHMC.jl and related packages.

Material for a workshop on Bayesian stats with R

Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Aesara

High-performance Bayesian Data Analysis on the GPU in Clojure

Collection of probabilistic models and inference algorithms

ParaMonte: Plain Powerful Parallel Monte Carlo and MCMC Library for Python, MATLAB, Fortran, C++, C.

Bayesian Evolutionary Analysis by Sampling Trees

Distributed Bayesian Entity Resolution in Apache Spark

Fast & scalable MCMC for all your exoplanet needs!

shinystan R package and ShinyStan GUI

identifying mutational significance in cancer genomes

R package to do the Ligand Receptor Analysis Visualization

Python package to annotate and visualize gene fusions.

Snakemake-based workflow for detecting structural variants in WGS data

Separating Normalizing Flows code from Pyro and improving API

Unix, R and python tools for genomics and data science

cBioPortal for Cancer Genomics

Clone identification from single-cell data

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Web client for CIViC: Clinical Interpretations of Variants in Cancer

Tree Approximate Message Passing

Simulating single-cell data using gene regulatory networks 📠

Fast inference for Gaussian processes in problems involving time. Partly built on results from https://proceedings.mlr.press/v161/tebbutt21a.html

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

REVOLVER - Repeated Evolution in Cancer

Companion package for the Coursera Statistics with R specialization

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

Genomics using open source tools, running on GCP or AWS

Cancer Predisposition Sequencing Reporter (CPSR)

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Backend server for Genome Nexus

Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit

[ WSDM '19 ] Sequential Variational Autoencoders for Collaborative Filtering

Scalable sparse Bayesian learning for large CS recovery problems

A Python package for approximate Bayesian inference and optimization using Gaussian processes

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

A novel management, annotation, and machine learning framework for analyzing cancer mutations