Pinned Repositories
cellrank
CellRank: dynamics from multi-view single-cell data
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.
scarches
Reference mapping for single-cell genomics
scgen
Single cell perturbation prediction
scib
Benchmarking analysis of data integration tools
scvelo
RNA Velocity generalized through dynamical modeling
single-cell-best-practices
https://www.sc-best-practices.org
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"
Theis Lab's Repositories
theislab/single-cell-best-practices
https://www.sc-best-practices.org
theislab/scarches
Reference mapping for single-cell genomics
theislab/scib
Benchmarking analysis of data integration tools
theislab/zellkonverter
Conversion between scRNA-seq objects
theislab/ehrapy
Electronic Health Record Analysis with Python.
theislab/anndata2ri
Convert between AnnData and SingleCellExperiment
theislab/moscot
Multi-omic single-cell optimal transport tools
theislab/nicheformer
Repository for Nicheformer: a foundation model for single-cell and spatial omics
theislab/hadge
Comprehensive pipeline for donor demultiplexing in single cell
theislab/spapros
Python package for Probe set selection for targeted spatial transcriptomics.
theislab/mubind
Learning motif contributions to cell transitions using sequence features and graphs.
theislab/geome
theislab/multigrate
Multigrate: multiomic data integration for single-cell genomics
theislab/scanpydoc
Collection of Sphinx extensions similar to (but more flexible than) numpydoc
theislab/inVAE
Invariant Representation learning
theislab/neural_organoid_atlas
Reproducibility repository for the Human Neural Organoid Atlas publication
theislab/IMPA
theislab/moscot_notebooks
Analysis notebooks using the moscot package
theislab/ehrapy-tutorials
Tutorials for ehrapy
theislab/jump-cpg0016-segmentation
Snakemake pipeline used to segment the cpg0016 dataset of the JUMP-Cell Painting Consortium
theislab/ehrdata
A datastructure for EHR data
theislab/ssl_in_scg
theislab/atlas-feature-selection-benchmark
Code for benchmarking the effect of feature selection on scRNA-seq atlas construction and use
theislab/svaeligr
sVAE with learnable interventions
theislab/gh-dashboard
A dashboard of everything in the theislab GitHub repository
theislab/moscot-framework_reproducibility
Data analysis for the moscot-framework project
theislab/sc_mae
theislab/transcription_factor_activity
theislab/ehrapy-reproducibility
theislab/masterpraktikum_ssl_segmentation
Repository accompanying the 2024 Masterpraktikum Project: Integrative Analysis of Histological Images and Gene Expression Data for Pathological Region Classification