theislab Goto Github PK

kbet

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

kbranches

Finding branching events and tips in single cell differentiation trajectories

lineagepulse

Differential expression analysis for single-cell RNA-seq data

lode

repository for all LODE projects

lungagingatlas

lunginjuryregeneration

masterpraktikum_ssl_segmentation

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

metamap

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

metamap-web

This interactive web tool facilitates exploration of the MetaMap resource (Simon et al. bioRxiv). In this large scale re-analysis raw RNA-seq data from over 400 studies relevant to human disease were screened for microbial and viral reads.

moscot

Multi-omic single-cell optimal transport tools

moscot-framework_reproducibility

Data analysis for the moscot-framework project

moscot_benchmarks

Benchmarks for moscot

moscot_neural_ot

Neural OT implementation into moscot

moscot_not

Implementation of Neural OT into moscot

moscot_notebooks

Analysis notebooks using the moscot package

moslin

Code, data and analysis for moslin.

mouse_cross-condition_pancreatic_islet_atlas

mrgr_stress_analysis

Repository for code and notebooks used for the analysis of the MRGR_Stress dataset from MPI for Psychiatry.

mubind

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

multicpa

multicpa-reproducibility

multigrate

Multigrate: multiomic data integration for single-cell genomics

multigrate_reproducibility

Reproducing results from Multigrate paper

multires-consensus-clustering

Code for the multi-resolution consensus clustering project

nbconvertr

Vignette Engine wrapping Jupyter Notebooks

ncem

Learning cell communication from spatial graphs of cells

ncem_benchmarks

ncem_tutorials

neural_organoid_atlas

Reproducibility repository for the Human Neural Organoid Atlas publication

openproblems-v2

Formalizing and benchmarking open problems in single-cell genomics