Theis Lab

scgen

Single cell perturbation prediction

diffxpy

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

scCODA

A Bayesian model for compositional single-cell data analysis

sfaira

data and model repository for single-cell data

ncem

Learning cell communication from spatial graphs of cells

destiny

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

batchglm

Fit generalized linear models in python.

scPoli_reproduce

Reproducibility notebooks for scPoli

tissue

tissue_tensorflow

theislab.github.io

theislab repository overview

2019_Strunz

Reproducibility repo accompanying Strunz et al. "Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis". Nat Commun. 2020.

cellrank_notebooks

Tutorials and examples for CellRank.

scatac_poisson_reproducibility

flowVI

flowVI: Flow Cytometry Variational Inference

covid-perturbation

feature-attribution-sc

perturbation-metrics

campa_ana

Analysis of 4i data from CAMPA manuscript

HRCA-reproducibility

Scripts related to the Human Retina Cell Atlas (Chen / Theis labs).

spatial_atlas_ssl

Self-supervised learning for mask inpainting on large spatial atlasses such as the BICCN 2.0 data.

ehrapy-site

sparsecca

Python implementations for Sparse CCA

filtration_curves

Code for the KDD 2021 paper 'Filtration Curves for Graph Representation'

ELS_analysis

Repository for code and notebooks for the analysis of the Early life adversity shapes social subordination and cell-type-specific transcriptomic (Kos et al., 2023) paper.

integraph

MRGR_stress_analysis

Repository for code and notebooks used for the analysis of the MRGR_Stress dataset from MPI for Psychiatry.

openproblems-v2

Formalizing and benchmarking open problems in single-cell genomics

scarches-1

Reference mapping for single-cell genomics

sfaira_extension