theislab

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"

https://www.sc-best-practices.org

RNA Velocity generalized through dynamical modeling

Benchmarking analysis of data integration tools

Reference mapping for single-cell genomics

Electronic Health Record Analysis with Python.

Single cell perturbation prediction

Deep count autoencoder for denoising scRNA-seq data

Mapping out the coarse-grained connectivity structures of complex manifolds.

Multi-omic single-cell optimal transport tools

Conversion between scRNA-seq objects

A Bayesian model for compositional single-cell data analysis

Differential expression analysis for single-cell RNA-seq data.

inferring regulatory cellular dynamics

Models and datasets for perturbational single-cell omics

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

Repository for Nicheformer: a foundation model for single-cell and spatial omics

Modeling complex perturbations with CellFlow

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of...

Convert between AnnData and SingleCellExperiment

LLM-powered personalized daily lists of scientific papers

data and model repository for single-cell data

Learning cell communication from spatial graphs of cells

R package for single cell and other data analysis using diffusion maps

Snakemake pipeline that works with the scIB package to benchmark data integration methods.

Unsupervised Deep Disentangled Representation of Single-Cell Omics

Additional code and analysis from the single-cell integration benchmarking project

Conditional out-of-distribution prediction

Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022

Reproducibility repository for the Human Neural Organoid Atlas publication

Python package for Probe set selection for targeted spatial transcriptomics.