Repository for Nicheformer: a foundation model for single-cell and spatial omics
☆165Nov 23, 2025Updated 6 months ago
Alternatives and similar repositories for nicheformer
Users that are interested in nicheformer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.☆103Mar 28, 2024Updated 2 years ago
- ☆138Feb 13, 2025Updated last year
- End-to-end analysis of spatial multi-omics data☆116May 15, 2026Updated 3 weeks ago
- ☆468Updated this week
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆82Nov 13, 2025Updated 7 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models☆79May 24, 2024Updated 2 years ago
- ☆13Sep 30, 2024Updated last year
- ☆413Nov 23, 2025Updated 6 months ago
- A tool for semi-automatic cell type harmonization and integration☆120Mar 9, 2026Updated 3 months ago
- ☆13Aug 9, 2022Updated 3 years ago
- Trends in single cell papers☆17Sep 23, 2024Updated last year
- UCE is a zero-shot foundation model for single-cell gene expression data☆255Feb 26, 2026Updated 3 months ago
- NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.☆24Jun 10, 2025Updated last year
- Perturbation-response Score (PS) analysis is a method to quantify diverse perturbation responses and discover novel biological insights i…☆17Apr 20, 2024Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ☆30Aug 29, 2025Updated 9 months ago
- Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.☆61May 30, 2024Updated 2 years ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆176May 25, 2026Updated 2 weeks ago
- ☆65Sep 13, 2024Updated last year
- Learning cell communication from spatial graphs of cells☆119Jan 15, 2024Updated 2 years ago
- Python code for cross-condition label refinement in single-cell data with HiDDEN☆14Sep 21, 2024Updated last year
- ☆13Sep 3, 2025Updated 9 months ago
- ☆15Apr 7, 2026Updated 2 months ago
- Deep fusion of spatial transcriptomics and histology images for interpretable high-definition embedding mapping☆18May 26, 2026Updated 2 weeks ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆54Mar 4, 2025Updated last year
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆147Feb 20, 2025Updated last year
- Reproducible analyses for the NicheCompass manuscript☆14Jul 3, 2025Updated 11 months ago
- A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.☆28Jan 3, 2025Updated last year
- ☆342May 23, 2025Updated last year
- ☆40Jun 24, 2025Updated 11 months ago
- Cell clustering and communication network inference for single-cell transcriptomics☆15Sep 18, 2024Updated last year
- ☆1,578Apr 29, 2026Updated last month
- Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab☆113Jul 4, 2025Updated 11 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆130Updated this week
- Non-parametric density inference for single-cell analysis.☆74Apr 10, 2026Updated 2 months ago
- ☆146Nov 6, 2025Updated 7 months ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆475Jun 6, 2025Updated last year
- an SRT simulator for simulating multiple spatial variability in spatial resolved transcriptomics and generating unbiased simulated SRT da…☆29Mar 11, 2025Updated last year
- ☆53Oct 9, 2025Updated 8 months ago
- Single Cell Pretrained Regulatory network INference from Transcripts☆11Sep 17, 2024Updated last year