Theis Lab

cellrank

CellRank: dynamics from multi-view single-cell data

scib

Benchmarking analysis of data integration tools

zellkonverter

Conversion between scRNA-seq objects

ehrapy

Electronic Health Record Analysis with Python.

anndata2ri

Convert between AnnData and SingleCellExperiment

moscot

Multi-omic single-cell optimal transport tools

pertpy

Perturbation Analysis in the scverse ecosystem.

nicheformer

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

hadge

Comprehensive pipeline for donor demultiplexing in single cell

spapros

Python package for Probe set selection for targeted spatial transcriptomics.

mubind

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

geome

multigrate

Multigrate: multiomic data integration for single-cell genomics

scanpydoc

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

inVAE

Invariant Representation learning

neural_organoid_atlas

Reproducibility repository for the Human Neural Organoid Atlas publication

IMPA

moscot_notebooks

Analysis notebooks using the moscot package

ehrapy-tutorials

Tutorials for ehrapy

ehrdata

A datastructure for EHR data

pertpy-tutorials

ssl_in_scg

atlas-feature-selection-benchmark

Code for benchmarking the effect of feature selection on scRNA-seq atlas construction and use

LungInjuryRegeneration

svaeligr

sVAE with learnable interventions

gh-dashboard

A dashboard of everything in the theislab GitHub repository

sc_mae

ehrapy-reproducibility

masterpraktikum_ssl_segmentation

Repository accompanying the 2024 Masterpraktikum Project: Integrative Analysis of Histological Images and Gene Expression Data for Pathological Region Classification

LungAgingAtlas