Lotfollahi-lab / nichecompassLinks
End-to-end analysis of spatial multi-omics data
☆101Updated 2 months ago
Alternatives and similar repositories for nichecompass
Users that are interested in nichecompass are comparing it to the libraries listed below
Sorting:
- ☆52Updated 2 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆147Updated last month
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆72Updated last month
- A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models☆75Updated last year
- Additional code and analysis from the single-cell integration benchmarking project☆71Updated 3 years ago
- A simulator for single cell multi-omics and spatial omics data that provides ground truth to benchmark a wide range of methods.☆67Updated 2 months ago
- ☆57Updated last year
- Spatial-Linked Alignment Tool☆90Updated last year
- a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution☆49Updated 4 months ago
- ☆60Updated last year
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆116Updated last year
- TACCO: Transfer of Annotations to Cells and their COmbinations☆62Updated 4 months ago
- scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics☆112Updated 3 months ago
- Code used to benchmark Xenium☆73Updated last year
- spatial transcriptome, single cell☆73Updated 2 years ago
- Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.☆146Updated 2 years ago
- Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics☆58Updated 7 months ago
- Spatially resolved transcriptomic analysis☆64Updated 3 years ago
- Predict RNA velocity through deep learning☆71Updated 2 years ago
- Probabilistic Alignment of Spatial Transcriptomics Experiments☆98Updated 10 months ago
- STAligner is a tool for alignment and integration of spatially resolved transcriptomics data.☆50Updated last year
- ☆127Updated last year
- Single cell omics biology annotations☆51Updated 8 months ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆80Updated 2 weeks ago
- overview of spatial datasets☆76Updated last year
- Spatial direct messaging detected by bivariate Moran☆32Updated 5 months ago
- Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets☆32Updated 2 years ago
- Cell cycle inference in single-cell RNA-seq☆51Updated 2 years ago
- ☆122Updated 7 months ago
- Python implementation of Milo for differential abundance testing on KNN graph☆77Updated 10 months ago