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Theis Lab (@theislab)

theislab

Stars
5,236
Global Org. Rank 4,409 (Top 2 %)
Registered about 8 years ago
Most used languages

Jupyter Notebook
64.5 %

Python
23.0 %

R
5.3 %

HTML
3.3 %

JavaScript
2.0 %

Nextflow 1.3 %

Others 0.7 %
Location 🇩🇪 Germany
Country Total Rank 289
Country Ranking

Nextflow 5

Jupyter Notebook
7

R
45

Python
87

HTML
165

Dockerfile
778

JavaScript
6,184

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

cellrank

CellRank: dynamics from multi-view single-cell data

scvelo

RNA Velocity generalized through dynamical modeling

scarches

Reference mapping for single-cell genomics

Jupyter Notebook

scib

Benchmarking analysis of data integration tools

scgen

Single cell perturbation prediction

dca

Deep count autoencoder for denoising scRNA-seq data

ehrapy

Electronic Health Record Analysis with Python.

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.

scCODA

A Bayesian model for compositional single-cell data analysis

Jupyter Notebook

sc-pert

Models and datasets for perturbational single-cell omics

Jupyter Notebook

sfaira

data and model repository for single-cell data

anndata2ri

Convert between AnnData and SingleCellExperiment

moscot

Multi-omic single-cell optimal transport tools

ncem

Learning cell communication from spatial graphs of cells

chemCPA

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

Jupyter Notebook

zellkonverter

Conversion between scRNA-seq objects

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.

scib-pipeline

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

destiny

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

nicheformer

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

Jupyter Notebook

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

scTab

Jupyter Notebook

tcellmatch

scArches-reproducibility

Reproducing result from the paper

Jupyter Notebook

graphcompass

GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems

Jupyter Notebook

deepflow

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

mubind

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

batchglm

Fit generalized linear models in python.

graph_abstraction

Generate cellular maps of differentiation manifolds with complex topologies.

Jupyter Notebook

DeepRT

Jupyter Notebook

hadge

Comprehensive pipeline for donor demultiplexing in single cell

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

spapros

Python package for Probe set selection for targeted spatial transcriptomics.

scvelo_notebooks

Jupyter Notebook

interactive_plotting

Jupyter Notebook

scgen-reproducibility

Jupyter Notebook

multimil

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

geome

campa

Conditional Autoencoders for Multiplexed Pixel Analysis

Jupyter Notebook

multicpa

scPoli_reproduce

Reproducibility notebooks for scPoli

Jupyter Notebook

cellrank_reproducibility

CellRank's reproducibility repository.

Jupyter Notebook

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

MetaMap

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

DeepCollisionalCrossSection

Jupyter Notebook

scAnalysisTutorial

Jupyter Notebook

multigrate

Multigrate: multiomic data integration for single-cell genomics

cross_system_integration

Jupyter Notebook

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

enrichment_analysis_celltype

Cell type enrichment analysis using gene signatures and cluster markers

ncem_tutorials

Jupyter Notebook

IMPA

Jupyter Notebook

diffxpy_tutorials

Tutorials for diffxpy.

Jupyter Notebook

moslin

Code, data and analysis for moslin.

Jupyter Notebook

trvaep

Jupyter Notebook

expiMap_reproducibility

Jupyter Notebook

ncem_benchmarks

Jupyter Notebook

greatpy

GREAT algorithm in Python

Jupyter Notebook

PathReg

Sparsity-enforcing regularizer

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

2020_Mayr

This repo contains the analysis code describing the findings of Mayr_et_al

Jupyter Notebook

ehrapy-tutorials

Tutorials for ehrapy

Jupyter Notebook

cpa-reproducibility

Notebooks for CPA figures

Jupyter Notebook

scachepy

Caching extension for Scanpy

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

scCODA_reproducibility

Jupyter Notebook

2018_Angelidis

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

gastrulation_analysis

Jupyter Notebook

trVAE_reproducibility

Jupyter Notebook

cellrank_notebooks

Tutorials and examples for CellRank.

Jupyter Notebook

intercode

Jupyter Notebook

spapros-pipeline

jump-cpg0016-segmentation

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

Jupyter Notebook

flowVI

flowVI: Flow Cytometry Variational Inference

sfaira_tutorials

Jupyter Notebook

theislab.github.io

theislab repository overview

scatac_poisson_reproducibility

Jupyter Notebook

disent

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

Jupyter Notebook

ehrapy-datasets

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

Jupyter Notebook

neural_organoid_atlas

Reproducibility repository for the Human Neural Organoid Atlas publication

Jupyter Notebook

moscot_notebooks

Analysis notebooks using the moscot package

Jupyter Notebook

scanpy-demo-czbiohub

single-cell scanpy teaching

kbranches

Finding branching events and tips in single cell differentiation trajectories

InterpretableAutoencoders

Jupyter Notebook

archmap

inVAE

Invariant Representation learning

Jupyter Notebook

cellrank_reproducibility_preprint

Code to reproduce results from the CellRank preprint

Jupyter Notebook

extended-single-cell-best-practices-container

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