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…☆291Updated this week
- Blood Transcription Modules for interpreting blood transcriptomics data☆11Nov 25, 2024Updated last year
- 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.
- 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 4 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.☆39Jul 7, 2026Updated last month
- R API and htmlwidget for Vitessce☆46Aug 13, 2025Updated last year
- Raw format to OME-TIFF converter☆58Updated this week
- 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☆108Sep 10, 2024Updated last year
- 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.
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆90Jul 4, 2026Updated last month
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆196Updated this week
- Finding gene expression states in scRNA-seq data☆56Mar 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☆159May 30, 2026Updated 3 months ago
- ☆45Oct 30, 2024Updated last year
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆189Updated this week
- Pyevolve☆14Dec 8, 2018Updated 7 years 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.
- scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.☆62Aug 5, 2026Updated 3 weeks ago
- 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☆387Updated this week
- SpatialCorr: Identify gene sets with spatially varying correlation☆18Jan 2, 2024Updated 2 years ago
- A post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping☆30Updated this week
- MCP server for spatial transcriptomics analysis through natural language interfaces.☆44Aug 15, 2026Updated 2 weeks ago
- Python library for plotting Cellphonedb results. Ported from ktplots R package.☆57Jun 29, 2026Updated 2 months ago
- 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.
- ☆17Sep 28, 2022Updated 3 years ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆187Updated 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 …☆481Jan 22, 2026Updated 7 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 2 years ago
- 🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.☆282Apr 26, 2026Updated 4 months ago
- tools in python and R for analyzing biological count data, especially from single cell RNAseq☆23Feb 1, 2024Updated 2 years ago