Projects in Awesome Lists by theislab

https://github.com/theislab/single-cell-tutorial

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"

Last synced: 15 May 2025

https://github.com/theislab/single-cell-best-practices

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

book rna-seq single-cell tutorial

Last synced: 11 Oct 2025

https://github.com/theislab/scvelo

RNA Velocity generalized through dynamical modeling

Last synced: 11 Oct 2025

https://github.com/theislab/cellrank

CellRank: dynamics from multi-view single-cell data

bioinformatics cell-fate-determination cell-fate-transitions data-science fuzzy-clustering-analyses genetics machine-learning manifold-learning markov-chains rna-velocity single-cell-genomics single-cell-rna-seq trajectory-generation

Last synced: 11 Oct 2025

https://github.com/theislab/scarches

Reference mapping for single-cell genomics

batch-correction data-integration deep-learning human-cell-atlas multimodal-deep-learning multiomics rna-seq-analysis scrna-seq single-cell single-cell-genomics

Last synced: 11 Oct 2025

https://github.com/theislab/single-cell-transformer-papers

Last synced: 14 Feb 2026

https://github.com/theislab/scgen

Single cell perturbation prediction

bioinformatics deep-learning generative-model scrna-seq single-cell single-cell-genomics transcriptomics

Last synced: 11 Oct 2025

https://github.com/theislab/ehrapy

Electronic Health Record Analysis with Python.

ehr electronic-health-record electronic-medical-record scverse

Last synced: 11 Oct 2025

https://github.com/theislab/moscot

Multi-omic single-cell optimal transport tools

optimal-transport single-cell

Last synced: 11 Oct 2025

https://github.com/theislab/sccoda

A Bayesian model for compositional single-cell data analysis

compositional-changes single-cell-rna-seq statistical-analysis tensorflow

Last synced: 11 Oct 2025

https://github.com/theislab/kbet

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

batch-effects data-science quantification scrnaseq

Last synced: 11 Oct 2025

https://github.com/theislab/sc-pert

Models and datasets for perturbational single-cell omics

Last synced: 11 Oct 2025

https://github.com/theislab/chemCPA

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

disentanglement drug-discovery genomics perturbation single-cell transfer-learning

Last synced: 09 May 2026

https://github.com/theislab/sfaira

data and model repository for single-cell data

Last synced: 11 Oct 2025

https://github.com/theislab/anndata2ri

Convert between AnnData and SingleCellExperiment

bioconductor jupyter rpy2 scanpy single-cell

Last synced: 16 May 2025

https://github.com/theislab/chemcpa

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

disentanglement drug-discovery genomics perturbation single-cell transfer-learning

Last synced: 11 Oct 2025

https://github.com/theislab/ncem

Learning cell communication from spatial graphs of cells

cell-cell-communication cell-cell-interaction cvae encoder-decoder-model glm gnn scanpy squidpy tensorflow

Last synced: 11 Oct 2025

https://github.com/theislab/cellflow

Modeling complex perturbations with CellFlow

Last synced: 11 Oct 2025

https://github.com/theislab/destiny

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

diffusion-maps dimensionality-reduction r

Last synced: 16 May 2025

https://github.com/theislab/nicheformer

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

Last synced: 11 Oct 2025

https://github.com/theislab/scib-pipeline

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

Last synced: 11 Oct 2025

https://github.com/theislab/paperbee

Last synced: 11 Oct 2025

https://github.com/theislab/trvae

Conditional out-of-distribution prediction

cvae deep-learning generative-model mmd single-cell

Last synced: 11 Oct 2025

https://github.com/theislab/scib-reproducibility

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

benchmarking integration results rna-seq scrna-seq single-cell website

Last synced: 11 Oct 2025

https://github.com/theislab/regvelo

inferring regulatory cellular dynamics

generative-model grn-inference perturbation-analysis rna-velocity-estimation single-cell-dynamics

Last synced: 11 Oct 2025

https://github.com/theislab/sctab

Last synced: 11 Oct 2025

https://github.com/theislab/drvi

Unsupervised Deep Disentangled Representation of Single-Cell Omics

anndata bioinformatics disentanglement integration python single-cell transcriptomics

Last synced: 02 Mar 2026

https://github.com/theislab/spatial_scog_workshop_2022

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

Last synced: 11 Oct 2025

https://github.com/theislab/pseudodynamics

Dynamic models for single-cell RNA-seq time series.

population-dynamics single-cell-analysis single-cell-rna-seq time-series

Last synced: 11 Oct 2025

https://github.com/theislab/graphcompass

GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems

Last synced: 05 Mar 2026

https://github.com/theislab/tcellmatch

Last synced: 11 Oct 2025

https://github.com/theislab/scvelo_notebooks

Last synced: 07 Mar 2026

https://github.com/theislab/prophet

Last synced: 10 Nov 2025

https://github.com/theislab/multimil

Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases

Last synced: 11 Oct 2025

https://github.com/theislab/deepflow

This code contains the neural network implementation from the nature communication manuscript NCOMMS-16-25447A.

Last synced: 11 Oct 2025

https://github.com/theislab/deeprt

Last synced: 11 Oct 2025

https://github.com/theislab/mubind

Learning motif contributions to cell transitions using sequence features and graphs.

Last synced: 11 Oct 2025

https://github.com/theislab/multigrate

Multigrate: multiomic data integration for single-cell genomics

Last synced: 11 Oct 2025

https://github.com/theislab/batchglm

Fit generalized linear models in python.

differential-expression generalized-linear-models tensorflow

Last synced: 11 Oct 2025

https://github.com/theislab/neural_organoid_atlas

Reproducibility repository for the Human Neural Organoid Atlas publication

Last synced: 11 Oct 2025

https://github.com/theislab/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"

Last synced: 11 Oct 2025

https://github.com/theislab/interactive_plotting

Last synced: 11 Oct 2025

https://github.com/theislab/invae

Invariant Representation learning

Last synced: 11 Oct 2025

https://github.com/theislab/campa

Conditional Autoencoders for Multiplexed Pixel Analysis

Last synced: 11 Oct 2025

https://github.com/theislab/geome

anndata graph-learning microscopy pytorch-geometric

Last synced: 11 Oct 2025

https://github.com/theislab/deepcollisionalcrosssection

Last synced: 11 Oct 2025

https://github.com/theislab/cellrank_reproducibility

CellRank's reproducibility repository.

genomics-data machine-learning reproducible-research single-cell

Last synced: 11 Oct 2025

https://github.com/theislab/greatpy

GREAT algorithm in Python

Last synced: 11 Oct 2025

https://github.com/theislab/scanpy-in-r

A guide to using the Python scRNA-seq analysis package Scanpy from R

guide interoperability python r scrna-seq tutorial

Last synced: 11 Oct 2025

https://github.com/theislab/cross_system_integration

Last synced: 11 Oct 2025

https://github.com/theislab/multicpa

Last synced: 11 Oct 2025

https://github.com/theislab/scpoli_reproduce

Reproducibility notebooks for scPoli

Last synced: 11 Oct 2025

https://github.com/theislab/ncem_tutorials

Last synced: 11 Oct 2025

https://github.com/theislab/cellink

Scalable framework for integrating single-cell omics with genetic data using AnnData.

anndata genetics single-cell

Last synced: 13 Feb 2026

https://github.com/theislab/gwas-scrnaseq-integration

A Shiny tool to define the cell-type of action by integrating single cell expression data with GWAS

Last synced: 11 Oct 2025

https://github.com/theislab/ssl_in_scg

Last synced: 11 Oct 2025

https://github.com/theislab/scanpydoc

Collection of Sphinx extensions similar to (but more flexible than) numpydoc

Last synced: 26 Jan 2026

https://github.com/theislab/moslin

Code, data and analysis for moslin.

cell genomics lineage optimal reproducible-research single tracing transport

Last synced: 11 Oct 2025

https://github.com/theislab/superexacttestpy

Python implementation of the SuperExactTest package

intersection python3 set statistics visualization

Last synced: 11 Oct 2025

https://github.com/theislab/diffxpy_tutorials

Tutorials for diffxpy.

Last synced: 11 Oct 2025

https://github.com/theislab/expimap_reproducibility

Last synced: 11 Oct 2025

https://github.com/theislab/scanalysistutorial

Last synced: 03 Mar 2026

https://github.com/theislab/cellrank2_reproducibility

CellRank 2's reproducibility repository.

Last synced: 11 Oct 2025

https://github.com/theislab/mapqc

MapQC - a metric for the evaluation of single-cell query-to-reference mappings

atlas integration mapping query-to-reference-mapping single-cell transcriptomics

Last synced: 11 Oct 2025

https://github.com/theislab/scatac_poisson_reproducibility

Last synced: 11 Oct 2025

https://github.com/theislab/enrichment_analysis_celltype

Cell type enrichment analysis using gene signatures and cluster markers

Last synced: 11 Oct 2025

https://github.com/theislab/mouse_cross-condition_pancreatic_islet_atlas

Last synced: 11 Oct 2025

https://github.com/theislab/sccoda_reproducibility

Last synced: 11 Oct 2025

https://github.com/theislab/jump-cpg0016-segmentation

Snakemake pipeline used to segment the cpg0016 dataset of the JUMP-Cell Painting Consortium

Last synced: 11 Oct 2025

https://github.com/theislab/moscot_notebooks

Analysis notebooks using the moscot package

Last synced: 11 Oct 2025

https://github.com/theislab/scachepy

Caching extension for Scanpy

Last synced: 16 Mar 2026

https://github.com/theislab/2018_angelidis

Reproducibility repo accompanying Angelidis et al. "An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics"

Last synced: 11 Oct 2025

https://github.com/theislab/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.

Last synced: 11 Oct 2025