Stars
Differential expression analysis for single-cell RNA-seq data.
Constructed attention-based deep multiple instance learning model using PyTorch and trained on 624 whole slide images of digitized H&E-stained prostate biopsies using AWS SageMaker’s data paralleli…
Tensors and Dynamic neural networks in Python with strong GPU acceleration
The fastai book, published as Jupyter Notebooks
Statistical Rethinking (2nd ed.) with NumPyro
Statistical Rethinking course and book package
brms R package for Bayesian generalized multivariate non-linear multilevel models using Stan
Uses Stan sampler and math library to semiparametrically fit linear and multilevel models with additive Bayesian Additive Regression Tree (BART) components.
Bayesian Data Analysis course at Aalto
Bayesian Data Analysis demos for Python
Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
Experimental design framework for scRNAseq population studies (eQTL and DE)
Exploratory analysis of Bayesian models with Python
DoWhy is a Python library for causal inference that supports explicit modeling and testing of causal assumptions. DoWhy is based on a unified language for causal inference, combining causal graphic…
A game theoretic approach to explain the output of any machine learning model.
Models and datasets for perturbational single-cell omics
Snakemake pipeline that works with the scIB package to benchmark data integration methods.
Deep universal probabilistic programming with Python and PyTorch
Additional code and analysis from the single-cell integration benchmarking project
Online variational Bayes for latent Dirichlet allocation (LDA)
PiGx SARS-CoV-2 wastewater sequencing pipeline
A tool to find sequencing data and metadata from public databases.
A scalable SCENIC workflow for single-cell gene regulatory network analysis
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis