A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and statistically enriched covariation of gene programs between interacting cell types from the neighborhood.
☆17Sep 25, 2026Updated 2 weeks ago
Alternatives and similar repositories for nico_tutorial
Users that are interested in nico_tutorial are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks☆35Aug 16, 2021Updated 5 years ago
- ☆35Jun 15, 2026Updated 3 months ago
- NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.☆23Jun 10, 2025Updated last year
- Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data☆18Apr 15, 2025Updated last year
- Cell clustering and communication network inference for single-cell transcriptomics☆14Sep 18, 2024Updated 2 years 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.
- Morphology-Enhanced Spatial Transcriptome Analysis Integrator☆26Mar 16, 2025Updated last year
- Gene Set Scoring on the Nearest Neighbor Graph (gssnng) for Single Cell RNA-seq (scRNA-seq) using AnnData h5ad files.☆12Oct 1, 2024Updated 2 years ago
- ☆28Jun 4, 2023Updated 3 years ago
- ☆22Sep 20, 2026Updated 2 weeks ago
- Python playground for cell-type-specific biology☆14Aug 25, 2026Updated last month
- A unified interface to spatial transcriptomics deconvolution tools☆56Aug 3, 2026Updated 2 months ago
- ☆39Sep 21, 2026Updated 2 weeks ago
- Single Cell Pretrained Regulatory network INference from Transcripts☆11Sep 17, 2024Updated 2 years ago
- ☆12May 24, 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.
- ☆13Sep 30, 2024Updated 2 years ago
- Detecting and dissecting anomalous anatomic regions in spatial transcriptomics with STANDS☆11May 18, 2026Updated 4 months ago
- Rmarkdown / compiled html files for human reprogramming dataset analysis☆18Jun 11, 2020Updated 6 years ago
- Hands-on training on the latest methodologies and applications for the analysis of nucleic acids from eukaryotic single cells☆17Jul 26, 2024Updated 2 years ago
- A computational tool for identification of 3D multi-modal spatial neighborhoods☆16Aug 1, 2025Updated last year
- ☆14Jun 10, 2025Updated last year
- Code of the paper "DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images"☆15May 12, 2026Updated 4 months ago
- Toolkit for metacell analysis☆24Aug 8, 2024Updated 2 years ago
- Viernes de Bioinformatica en el LIIGH, 2 febrero - 2 de agosto 2024☆27Oct 24, 2025Updated 11 months ago
- 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.
- Scripts from the GBM cellular states paper☆21Feb 24, 2021Updated 5 years ago
- Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data☆79Jan 17, 2025Updated last year
- Deciphering cell-cell communication from spatially resolved transcriptomic data at single-cell resolution with subgraph-based attentional…☆30Sep 6, 2024Updated 2 years ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆197Updated this week
- Spatial direct messaging detected by bivariate Moran☆33Jul 16, 2025Updated last year
- Cell-type Relationship Analysis Workflow Done Across Distances☆42Nov 18, 2025Updated 10 months ago
- scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.☆64Sep 17, 2026Updated 3 weeks ago
- Algorithmic and Utility Extensions for the Imaris Program☆21Aug 28, 2026Updated last month
- scID☆14Oct 21, 2021Updated 4 years 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.
- A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data☆86Jul 25, 2025Updated last year
- ☆23Sep 20, 2022Updated 4 years ago
- ☆16Sep 29, 2023Updated 3 years ago
- EnrichMap: Spatially-informed enrichment analysis for functional interpretation of spatial transcriptomics.☆17Jun 26, 2026Updated 3 months ago
- JAX Scalify: end-to-end scaled arithmetics☆18Oct 30, 2024Updated last year
- Framework for analysis of cell-types and Ligand-Receptor cooccurrences☆21Feb 13, 2023Updated 3 years ago
- ☆13Oct 7, 2024Updated 2 years ago