End-to-end analysis of spatial multi-omics data
☆114Jan 26, 2026Updated 3 months ago
Alternatives and similar repositories for nichecompass
Users that are interested in nichecompass are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Reproducible analyses for the NicheCompass manuscript☆14Jul 3, 2025Updated 10 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆173Apr 27, 2026Updated last week
- ☆53Oct 9, 2025Updated 6 months ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆129Updated this week
- Repository for Nicheformer: a foundation model for single-cell and spatial omics☆161Nov 23, 2025Updated 5 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Automatically annotate cell types, consistently across samples.☆20Updated this week
- ☆13Nov 3, 2023Updated 2 years ago
- ☆149Mar 20, 2026Updated last month
- scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (e…☆31Aug 20, 2025Updated 8 months ago
- ☆15Jun 27, 2025Updated 10 months ago
- Hotspot cluster distance analysis in spatial transcriptomic data☆37Feb 10, 2025Updated last year
- scMalignantFinder is a Python package specially designed for analyzing cancer single-cell RNA-seq datasets to distinguish malignant cells…☆18Mar 27, 2026Updated last month
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆122Jan 22, 2024Updated 2 years ago
- Scanner of specific spatial patterns in tissues☆14Jul 15, 2022Updated 3 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆430Apr 11, 2026Updated 3 weeks ago
- Spatiotemporal modeling of spatial transcriptomics☆337Feb 25, 2026Updated 2 months ago
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics☆49Aug 18, 2025Updated 8 months ago
- Tumour Heterogeneity and Intercellular Networks of Nasopharyngeal Carcinoma at Single Cell Resolution☆13Mar 1, 2023Updated 3 years ago
- Join subcellular Visium HD bins into cells☆141Nov 4, 2025Updated 6 months ago
- CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data☆35Jul 24, 2025Updated 9 months ago
- BANKSY: spatial clustering☆142Updated this week
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆78Nov 13, 2025Updated 5 months ago
- ☆34Feb 25, 2025Updated last year
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- ☆37Oct 22, 2025Updated 6 months ago
- Aligning gene expression trajectories of single-cell reference and query systems☆88Aug 10, 2025Updated 8 months ago
- LIANA+: an all-in-one framework for cell-cell communication☆284Jan 24, 2026Updated 3 months ago
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆91Mar 16, 2026Updated last month
- Spatial Single Cell Analysis in Python☆567Updated this week
- Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms☆195Jan 30, 2026Updated 3 months ago
- Package for the analysis of Transcripts outside segmented cells in ST data☆28Apr 27, 2026Updated last week
- A Bayesian model for compositional single-cell data analysis☆195Jan 13, 2026Updated 3 months ago
- Reference mapping for single-cell genomics☆404Mar 21, 2026Updated last month
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆67Nov 6, 2024Updated last year
- Network analyses of single cell-based digital twins for personalized treatment of inflammatory disease☆15Mar 23, 2024Updated 2 years ago
- Spot pseudo-Imager on top of histology☆49Dec 12, 2025Updated 4 months ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆141Feb 20, 2025Updated last year
- Modular pipeline for integrated analysis of the tumour microenvironment using multiplex imaging☆14Jul 29, 2025Updated 9 months ago
- Non-parametric density inference for single-cell analysis.☆73Apr 10, 2026Updated 3 weeks ago
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆360Updated this week