NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.
☆23Jun 10, 2025Updated last year
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:
- Python playground for cell-type-specific biology☆14Jul 10, 2026Updated last month
- Compute the neighborhood consolidation matrix and identify SHRs☆15Jun 12, 2025Updated last year
- Tumor-Infiltrating CD8 Lymphocytes states prediction☆14Feb 7, 2024Updated 2 years ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆187Aug 10, 2026Updated last week
- A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and …☆16Aug 11, 2026Updated last week
- 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☆15Apr 29, 2025Updated last year
- End-to-end analysis of spatial multi-omics data☆123May 15, 2026Updated 3 months ago
- ☆16Sep 29, 2023Updated 2 years ago
- Clonalscope is a subclone detection method based on copy number alterations (CNAs) for single-cell and ST tumor sequencing data. Clonalsc…☆32Sep 30, 2025Updated 10 months ago
- ☆11Jul 8, 2024Updated 2 years ago
- ☆18Nov 24, 2024Updated last year
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆477Jan 22, 2026Updated 6 months ago
- Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separ…☆32Mar 10, 2023Updated 3 years ago
- ☆22Jan 6, 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.
- A package for analyzing spatial transcriptomics data with Gaussian smoothing, spatial gene correlation network clustering, gene module vi…☆22Apr 3, 2026Updated 4 months ago
- ☆21Jul 7, 2026Updated last month
- a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution☆55Aug 11, 2025Updated last year
- End-to-end model for cell segmentation and classification☆23Jan 13, 2025Updated last year
- MorphLink: Bridging Cellular Morphological Behaviors and Molecular Dynamics in Multi-modal Spatial Omics☆18Dec 7, 2025Updated 8 months ago
- ☆30Oct 4, 2024Updated last year
- R package for Pathway RespOnsive GENe activity inference☆127Jan 30, 2023Updated 3 years ago
- ☆15Jun 27, 2025Updated last year
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆195Aug 12, 2025Updated last year
- 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.
- Multi-slice Spatial Transcriptome Domain Analysis.☆13Dec 13, 2024Updated last year
- ImgLib2 RealTransform brought to QuPath☆34Mar 12, 2026Updated 5 months ago
- COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data…☆70Jul 28, 2026Updated 3 weeks ago
- R package to infer biological activities from omics data using a collection of methods.☆304Dec 16, 2025Updated 8 months ago
- An R package for performing cell typing in SMI and other single cell data☆53May 1, 2026Updated 3 months ago
- Spatial omics analysis toolbox☆387Updated this week
- a deep generative model for single-cell survival analysis☆26Dec 2, 2025Updated 8 months ago
- ☆14Jun 10, 2025Updated last year
- ☆74May 28, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics☆50Aug 18, 2025Updated 11 months ago
- Collection of useful methods for single cell analysis☆15Aug 22, 2024Updated last year
- ☆13Aug 3, 2026Updated 2 weeks ago
- ☆38Jan 22, 2026Updated 6 months ago
- Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spat…☆36Nov 30, 2023Updated 2 years ago
- Cell-type Relationship Analysis Workflow Done Across Distances☆42Nov 18, 2025Updated 8 months ago
- Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.☆86May 22, 2026Updated 2 months ago