Theis Lab

scvelo

RNA Velocity generalized through dynamical modeling

scarches

Reference mapping for single-cell genomics

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

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

IMPA

moscot_notebooks

Analysis notebooks using the moscot package

ehrapy-tutorials

Tutorials for ehrapy

jump-cpg0016-segmentation

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

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

LungAgingAtlas