Theis Lab

AutoGeneS

scArches-reproducibility

Reproducing result from the paper

scvelo_notebooks

Covid_meta_analysis

Analysis notebooks for the Covid-19 meta analysis that accompanies the Nature Medicine publication "Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics"

cellrank_reproducibility

CellRank's reproducibility repository.

squidpy_reproducibility

gastrulation_analysis

spapros-pipeline

2020_Mayr

This repo contains the analysis code describing the findings of Mayr_et_al

disent

Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing data

intercode

InterpretableAutoencoders

cellrank_reproducibility_preprint

Code to reproduce results from the CellRank preprint

sc_analysis_template

Template repository for standard single-cell data analysis

2020_iPS_Lung_Differentiation

Reproducibility repo accompanying Chaido Ori, Meshal Ansari, Ilias Angelidis, Fabian J. Theis, Herbert B. Schiller and Micha Drukker "Single cell trajectory mapping of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors".

2021_Aliluev_Tritschler_gut_HFD

bartseq-pipeline

Demultiplexing pipeline for BART-Seq

covid_macrophages_integration

scRNA-seq data integration from "SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis".

gut_lineage

scanpy_squidpy_demo_2021

2021_PRMT7_regulates_Monocyte_Extravasation

astrocytes_reprogramming_analysis

autoencoderPS

GoBI_single_cell

Single-cell worksheet and notes for the GoBI bachelor course 2021

organoid_dexamethason_stimulation

Code accompanying publication https://doi.org/10.1176/appi.ajp.2021.21010095

sc_ketamine_analysis

scRNA-seq analyses for the ketamine project

scanpy.org

sfaira-portal

Code for the Sfaira Portal website

sfaira-site

Website displaying the sfaira database

sfaira_benchmarks