End-to-end analysis of spatial multi-omics data
☆129Oct 4, 2026Updated last week
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:
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆197Updated this week
- Generation of disentangled microenvironment-induced and intrinsic gene expression vectors from spatial transcriptomics data☆27Jul 3, 2026Updated 3 months ago
- Reproducible analyses for the NicheCompass manuscript☆15Oct 5, 2026Updated last week
- a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution☆56Aug 11, 2025Updated last year
- Fairness in single-cell data☆21Mar 25, 2026Updated 6 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆31Apr 15, 2026Updated 5 months ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆162Sep 18, 2026Updated 3 weeks ago
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆100Jul 4, 2026Updated 3 months ago
- ☆57Sep 2, 2026Updated last month
- NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.☆23Jun 10, 2025Updated last year
- Package for the analysis of Transcripts outside segmented cells in ST data☆31Oct 5, 2026Updated last week
- Repository for Nicheformer: a foundation model for single-cell and spatial omics☆175Nov 23, 2025Updated 10 months ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆296Updated this week
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆90Oct 6, 2026Updated last week
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- ☆39Jan 22, 2026Updated 8 months ago
- ☆19Sep 19, 2025Updated last year
- ☆166Mar 20, 2026Updated 6 months ago
- scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (e…☆39Aug 15, 2026Updated last month
- ☆15Jun 27, 2025Updated last year
- Spatiotemporal modeling of spatial transcriptomics☆344Feb 25, 2026Updated 7 months ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆193Sep 22, 2026Updated 3 weeks ago
- A Snakemake pipeline for Xenium data analysis.☆28Jul 22, 2026Updated 2 months ago
- BANKSY: spatial clustering☆166Sep 29, 2026Updated 2 weeks ago
- 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.
- Automatically annotate cell types, consistently across samples.☆30Updated this week
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆125Jan 22, 2024Updated 2 years ago
- ☆22Jan 6, 2024Updated 2 years ago
- ☆13Nov 3, 2023Updated 2 years ago
- A Bayesian model for compositional single-cell data analysis☆203Jan 13, 2026Updated 9 months ago
- LIANA+: an all-in-one framework for cell-cell communication☆321Updated this week
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆202Aug 12, 2025Updated last year
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆477Apr 11, 2026Updated 6 months ago
- Profile purification of single-cell spatial transcriptomics data☆64Jun 29, 2026Updated 3 months ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Join subcellular Visium HD bins into cells☆145Sep 14, 2026Updated last month
- GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data☆76Dec 1, 2025Updated 10 months ago
- An R package for performing cell typing in SMI and other single cell data☆56May 1, 2026Updated 5 months ago
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆401Updated this week
- Spatial Single Cell Analysis in Python☆601Oct 7, 2026Updated last week
- ☆64Aug 6, 2025Updated last year
- ☆28Oct 7, 2026Updated last week