NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.
☆24Jun 10, 2025Updated 11 months ago
Alternatives and similar repositories for NicheDE
Users that are interested in NicheDE 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 package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and …☆16Dec 5, 2025Updated 5 months ago
- Clonalscope is a subclone detection method based on copy number alterations (CNAs) for single-cell and ST tumor sequencing data. Clonalsc…☆29Sep 30, 2025Updated 7 months ago
- Compute the neighborhood consolidation matrix and identify SHRs☆14Jun 12, 2025Updated 11 months ago
- Python playground for cell-type-specific biology☆14May 11, 2026Updated 2 weeks ago
- Tumor-Infiltrating CD8 Lymphocytes states prediction☆14Feb 7, 2024Updated 2 years 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.
- BayesTME: A reference-free Bayesian method for analyzing spatial transcriptomics data☆14Apr 29, 2025Updated last year
- ☆11Jul 8, 2024Updated last year
- a deep generative model for single-cell survival analysis☆26Dec 2, 2025Updated 5 months ago
- ☆18Nov 24, 2024Updated last year
- End-to-end model for cell segmentation and classification☆23Jan 13, 2025Updated last year
- Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spat…☆33Nov 30, 2023Updated 2 years ago
- An R package for performing cell typing in SMI and other single cell data☆49May 1, 2026Updated 3 weeks ago
- ☆18Jan 6, 2024Updated 2 years ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆458Jan 22, 2026Updated 4 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.
- Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separ…☆33Mar 10, 2023Updated 3 years ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆173May 18, 2026Updated last week
- ☆21Jul 7, 2025Updated 10 months ago
- This repository is for CellBin research group☆37Updated this week
- R package for Pathway RespOnsive GENe activity inference☆124Jan 30, 2023Updated 3 years ago
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆188Aug 12, 2025Updated 9 months ago
- ☆30Oct 4, 2024Updated last year
- Multi-slice Spatial Transcriptome Domain Analysis.☆13Dec 13, 2024Updated last year
- ☆15Jun 27, 2025Updated 11 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution☆53Aug 11, 2025Updated 9 months ago
- COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data…☆69Mar 17, 2026Updated 2 months ago
- Repository for Nicheformer: a foundation model for single-cell and spatial omics☆163Nov 23, 2025Updated 6 months ago
- A R/MATLAB package to construct and compare gene regulatory networks from single-cell transcriptomic data☆36Mar 26, 2026Updated 2 months ago
- ☆35Jan 9, 2024Updated 2 years ago
- R package to infer biological activities from omics data using a collection of methods.☆294Dec 16, 2025Updated 5 months ago
- Spatial omics analysis toolbox☆374Updated this week
- Learning meaningful representations of genes☆21Jul 7, 2025Updated 10 months ago
- ☆100May 4, 2026Updated 3 weeks ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Identification of spatial homogeneous regions☆21Oct 6, 2025Updated 7 months ago
- ☆73May 28, 2025Updated last year
- ☆20Jul 30, 2024Updated last year
- ☆17Mar 18, 2025Updated last year
- Collection of useful methods for single cell analysis☆15Aug 22, 2024Updated last year
- ☆12May 14, 2026Updated 2 weeks ago
- R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data☆36Jan 13, 2026Updated 4 months ago