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Theis Lab (@theislab)

theislab

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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"

Jupyter Notebook

single-cell-best-practices

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

Jupyter Notebook

scvelo

RNA Velocity generalized through dynamical modeling

scarches

Reference mapping for single-cell genomics

Jupyter Notebook

cellrank

CellRank: dynamics from multi-view single-cell data

scib

Benchmarking analysis of data integration tools

scgen

Single cell perturbation prediction

dca

Deep count autoencoder for denoising scRNA-seq data

diffxpy

Differential expression analysis for single-cell RNA-seq data.

paga

Mapping out the coarse-grained connectivity structures of complex manifolds.

Jupyter Notebook

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

scCODA

A Bayesian model for compositional single-cell data analysis

Jupyter Notebook

sc-pert

Models and datasets for perturbational single-cell omics

Jupyter Notebook

anndata2ri

Convert between AnnData and SingleCellExperiment

ehrapy

Electronic Health Record Analysis with Python.

ncem

Learning cell communication from spatial graphs of cells

moscot

Multi-omic single-cell optimal transport tools

zellkonverter

Conversion between scRNA-seq objects

chemCPA

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

Jupyter Notebook

pertpy

Perturbation Analysis in the scverse ecosystem.

cpa

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

destiny

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

scib-pipeline

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

trVAE

Conditional out-of-distribution prediction

scib-reproducibility

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

Jupyter Notebook

AutoGeneS

Jupyter Notebook

spatial_scog_workshop_2022

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

Jupyter Notebook

pseudodynamics

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

Jupyter Notebook

tcellmatch

scArches-reproducibility

Reproducing result from the paper

Jupyter Notebook

deepflow

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

batchglm

Fit generalized linear models in python.

graph_abstraction

Generate cellular maps of differentiation manifolds with complex topologies.

Jupyter Notebook

scTab

Jupyter Notebook

DeepRT

Jupyter Notebook

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"

Jupyter Notebook

scvelo_notebooks

Jupyter Notebook

spapros

Python package for Probe set selection for targeted spatial transcriptomics.

interactive_plotting

Jupyter Notebook

mubind

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

nicheformer

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

Jupyter Notebook

hadge

Comprehensive pipeline for donor demultiplexing in single cell

scgen-reproducibility

Jupyter Notebook

graphcompass

GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems

Jupyter Notebook

geome

campa

Conditional Autoencoders for Multiplexed Pixel Analysis

Jupyter Notebook

cellrank_reproducibility

CellRank's reproducibility repository.

Jupyter Notebook

multicpa

scanpy-in-R

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

scanpydoc

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

scPoli_reproduce

Reproducibility notebooks for scPoli

Jupyter Notebook

DeepCollisionalCrossSection

Jupyter Notebook

MetaMap

The code and analyses accompanying the manuscript “MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data”.

scAnalysisTutorial

Jupyter Notebook

multigrate

Multigrate: multiomic data integration for single-cell genomics

GWAS-scRNAseq-Integration

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

superexacttestpy

Python implementation of the SuperExactTest package

Jupyter Notebook

ncem_tutorials

Jupyter Notebook

enrichment_analysis_celltype

Cell type enrichment analysis using gene signatures and cluster markers

moslin

Code, data and analysis for moslin.

Jupyter Notebook

diffxpy_tutorials

Tutorials for diffxpy.

Jupyter Notebook

cross_system_integration

Jupyter Notebook

expiMap_reproducibility

Jupyter Notebook

trvaep

Jupyter Notebook

greatpy

GREAT algorithm in Python

Jupyter Notebook

PathReg

Sparsity-enforcing regularizer

Jupyter Notebook

IMPA

Jupyter Notebook

ncem_benchmarks

Jupyter Notebook

squidpy_reproducibility

Jupyter Notebook

sc-best-practices-ce

The best-practices workflow for single-cell RNA-seq analysis as determined by the community.

tissue_tensorflow

scachepy

Caching extension for Scanpy

Jupyter Notebook

cpa-reproducibility

Notebooks for CPA figures

Jupyter Notebook

scCODA_reproducibility

Jupyter Notebook

2020_Mayr

This repo contains the analysis code describing the findings of Mayr_et_al

Jupyter Notebook

gastrulation_analysis

Jupyter Notebook

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.

Jupyter Notebook

trVAE_reproducibility

Jupyter Notebook

cellrank_notebooks

Tutorials and examples for CellRank.

Jupyter Notebook

moscot_notebooks

Analysis notebooks using the moscot package

Jupyter Notebook

intercode

Jupyter Notebook

spapros-pipeline

ehrapy-tutorials

Tutorials for ehrapy

Jupyter Notebook

sfaira_tutorials

Jupyter Notebook

flowVI

flowVI: Flow Cytometry Variational Inference

2018_Angelidis

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

InterpretableAutoencoders

Jupyter Notebook

theislab.github.io

theislab repository overview

disent

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

Jupyter Notebook

neural_organoid_atlas

Reproducibility repository for the Human Neural Organoid Atlas publication

Jupyter Notebook

ehrapy-datasets

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

Jupyter Notebook

scatac_poisson_reproducibility

Jupyter Notebook

scanpy-demo-czbiohub

single-cell scanpy teaching

kbranches

Finding branching events and tips in single cell differentiation trajectories

jump-cpg0016-segmentation

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

Jupyter Notebook

cellrank_reproducibility_preprint

Code to reproduce results from the CellRank preprint

Jupyter Notebook

inVAE

Invariant Representation learning

Jupyter Notebook

extended-single-cell-best-practices-container

Hosting the container for the extended single-cell best-practices book

perturbation-metrics

Jupyter Notebook