Lotfollahi-lab / nichecompass
End-to-end analysis of spatial multi-omics data
☆41Updated last month
Alternatives and similar repositories for nichecompass:
Users that are interested in nichecompass are comparing it to the libraries listed below
- ☆45Updated this week
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆34Updated last week
- Spatial direct messaging detected by bivariate Moran☆25Updated 2 months ago
- Additional code and analysis from the single-cell integration benchmarking project☆59Updated 2 years ago
- ☆57Updated 6 months ago
- ☆42Updated 3 months ago
- Single cell omics biology annotations☆50Updated last week
- single cell foundation model for Gene network inference and more☆56Updated this week
- Bayesian Analytics for Spatial Segmentation☆25Updated 5 months ago
- ☆45Updated 2 years ago
- Predict RNA velocity through deep learning☆66Updated last year
- Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets☆30Updated last year
- Code used to benchmark Xenium☆51Updated 8 months ago
- Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics☆39Updated 2 weeks ago
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆61Updated 10 months ago
- Python implementation of Milo for differential abundance testing on KNN graph☆63Updated last month
- Probabilistic Alignment of Spatial Transcriptomics Experiments v.2☆34Updated 2 weeks ago
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆40Updated 3 years ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆54Updated last week
- A python port of the R package SCTransform:☆19Updated 3 years ago
- ☆47Updated last year
- Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).☆20Updated last month
- Reproducing the experiments of the DestVI paper☆18Updated 3 years ago
- SPROD: Spatial expression profiling de-noising☆36Updated last year
- UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference☆26Updated 4 months ago
- ☆26Updated last year
- Gene group activity utility functions for Scanpy☆71Updated 2 months ago
- TACCO: Transfer of Annotations to Cells and their COmbinations☆45Updated 8 months ago
- Deconvoluting Spatial Transcriptomics Data through Graph-based Artificial Intelligence☆37Updated 2 years ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆61Updated 6 months ago