Analyzing cellular niches in spatial transcriptomics data
☆38Nov 18, 2024Updated last year
Alternatives and similar repositories for monkeybread
Users that are interested in monkeybread are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Simple Jupyter chat UI for LangChain☆10Jul 3, 2024Updated 2 years ago
- ☆19Apr 20, 2025Updated last year
- Identification of persistent local patterns in spatial omics data☆18May 6, 2025Updated last year
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆290Jul 15, 2026Updated 3 weeks ago
- Blood Transcription Modules for interpreting blood transcriptomics data☆11Nov 25, 2024Updated last year
- 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.
- Inference of TCR motifs☆33Jun 17, 2025Updated last year
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆41Apr 30, 2026Updated 3 months ago
- BIRDS plug-in on Fiji and attached jar package☆22Oct 7, 2021Updated 4 years ago
- A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.☆38Jul 7, 2026Updated last month
- R API and htmlwidget for Vitessce☆45Aug 13, 2025Updated 11 months ago
- Raw format to OME-TIFF converter☆57Jul 27, 2026Updated 2 weeks ago
- Package for the analysis of Transcripts outside segmented cells in ST data☆31Updated this week
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆46Jun 13, 2025Updated last year
- Analysis of cell-cell communication at single-cell resolution☆107Sep 10, 2024Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆87Jul 4, 2026Updated last month
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆194Mar 27, 2025Updated last year
- Finding gene expression states in scRNA-seq data☆54Mar 22, 2024Updated 2 years ago
- Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq☆13Apr 2, 2024Updated 2 years ago
- ☆13Jun 6, 2024Updated 2 years ago
- BANKSY: spatial clustering☆158May 30, 2026Updated 2 months ago
- ☆45Oct 30, 2024Updated last year
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆185Jul 26, 2026Updated 2 weeks ago
- Pyevolve☆14Dec 8, 2018Updated 7 years 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.
- scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.☆62Updated this week
- CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data☆35Jul 24, 2025Updated last year
- Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.☆18Aug 8, 2025Updated last year
- ☆18Mar 31, 2024Updated 2 years ago
- An open and interoperable data framework for spatial omics data☆383Updated this week
- A post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping☆29Updated this week
- MCP server for spatial transcriptomics analysis through natural language interfaces.☆43Updated this week
- Python library for plotting Cellphonedb results. Ported from ktplots R package.☆57Jun 29, 2026Updated last month
- ☆17Sep 28, 2022Updated 3 years 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.
- Probabilistic cell segmentation for in situ spatial transcriptomics☆182Updated this week
- Detect hierarchical structures in cell-cell communications☆16Jan 26, 2025Updated last year
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆474Jan 22, 2026Updated 6 months ago
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆63Aug 17, 2024Updated last year
- 🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.☆281Apr 26, 2026Updated 3 months ago
- tools in python and R for analyzing biological count data, especially from single cell RNAseq☆23Feb 1, 2024Updated 2 years ago
- Hierarchical Random Forest for Information Transfer☆13May 26, 2021Updated 5 years ago