Theis Lab

dca

Deep count autoencoder for denoising scRNA-seq data

scCODA

A Bayesian model for compositional single-cell data analysis

kBET

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

sfaira

data and model repository for single-cell data

ncem

Learning cell communication from spatial graphs of cells

scPoli_reproduce

Reproducibility notebooks for scPoli

scatac_poisson_reproducibility

tissue_tensorflow

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.

ehrapy-datasets

A collection of scripts to generate AnnData objects of EHR datasets for ehrapy

theislab.github.io

theislab repository overview

flowVI

flowVI: Flow Cytometry Variational Inference

singlecell_proteomics

spatial_atlas_ssl

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

covid-perturbation

feature-attribution-sc

perturbation-metrics

moscot_not

Implementation of Neural OT into moscot

HRCA-reproducibility

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

tissue

ehrapy-site

idtrack

Cross-Temporal and Cross-Database Biological Identifier Mapping

sparsecca

Python implementations for Sparse CCA

filtration_curves

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

2015-grn-inference

Andrea Ocone’s GRN inference framework

archmap_admin

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

openproblems-v2

Formalizing and benchmarking open problems in single-cell genomics

scarches-1

Reference mapping for single-cell genomics