Analyzing cellular niches in spatial transcriptomics data
☆35Nov 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:
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆275Updated this week
- Simple Jupyter chat UI for LangChain☆11Jul 3, 2024Updated last year
- Identification of persistent local patterns in spatial omics data☆15May 6, 2025Updated 11 months ago
- ☆19Apr 20, 2025Updated last year
- A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.☆34Apr 6, 2026Updated 3 weeks ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆171Mar 16, 2026Updated last month
- Blood Transcription Modules for interpreting blood transcriptomics data☆11Nov 25, 2024Updated last year
- Inference of TCR motifs☆32Jun 17, 2025Updated 10 months ago
- R API and htmlwidget for Vitessce☆45Aug 13, 2025Updated 8 months ago
- BIRDS plug-in on Fiji and attached jar package☆22Oct 7, 2021Updated 4 years ago
- Package for the analysis of Transcripts outside segmented cells in ST data☆28Apr 20, 2026Updated last week
- An open and interoperable data framework for spatial omics data☆363Apr 20, 2026Updated last week
- ☆17Sep 28, 2022Updated 3 years ago
- Assembly and Annotation of the Human Immune Health Atlas☆24Aug 28, 2025Updated 8 months ago
- 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.
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆36Sep 20, 2024Updated last year
- Analysis of cell-cell communication at single-cell resolution☆107Sep 10, 2024Updated last year
- Detect hierarchical structures in cell-cell communications☆16Jan 26, 2025Updated last year
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆46Jun 13, 2025Updated 10 months ago
- Raw format to OME-TIFF converter☆57Updated this week
- ☆13Jun 6, 2024Updated last year
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆187Mar 27, 2025Updated last year
- Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq☆13Apr 2, 2024Updated 2 years ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆128Updated this week
- 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.
- Probabilistic cell segmentation for in situ spatial transcriptomics☆167Updated this week
- BANKSY: spatial clustering☆141Oct 15, 2025Updated 6 months ago
- ☆28Updated this week
- Python Toolkit for Transcription Factor Activity Inference and Clustering of scRNA-seq Data☆36Dec 15, 2025Updated 4 months ago
- ☆45Oct 30, 2024Updated last year
- Finding gene expression states in scRNA-seq data☆51Mar 22, 2024Updated 2 years ago
- Deep learning based spot detection for FISH images.☆34Jan 7, 2026Updated 3 months ago
- Pyevolve☆14Dec 8, 2018Updated 7 years ago
- Code used to benchmark Xenium☆80Apr 10, 2026Updated 2 weeks ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.☆18Aug 8, 2025Updated 8 months ago
- SpatialCorr: Identify gene sets with spatially varying correlation☆18Jan 2, 2024Updated 2 years ago
- Python package for Probe set selection for targeted spatial transcriptomics.☆48Nov 8, 2025Updated 5 months ago
- ☆19Mar 31, 2024Updated 2 years ago
- Python library for plotting Cellphonedb results. Ported from ktplots R package.☆57Mar 16, 2026Updated last month
- A post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping☆29Apr 5, 2026Updated 3 weeks ago
- ☆25Dec 5, 2025Updated 4 months ago