A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data
☆41Jun 26, 2026Updated 3 weeks ago
Alternatives and similar repositories for spatialaxe
Users that are interested in spatialaxe are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Nextflow version of Sopa - spatial omics pipeline and analysis☆18Updated this week
- Single-cell differential expression☆19Apr 23, 2026Updated 2 months ago
- Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…☆77Jun 22, 2026Updated 3 weeks ago
- A Python package for unsupervised analysis of spatial (prote)omics data.☆17Updated this week
- Python API and Jupyter widget for Vitessce☆67Jun 10, 2026Updated last month
- 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.
- Spatial omics analysis and visualization library☆27Updated this week
- Automatically annotate cell types, consistently across samples.☆25Jul 13, 2026Updated last week
- An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.☆15Nov 3, 2025Updated 8 months ago
- ☆18May 15, 2026Updated 2 months ago
- Profile purification of single-cell spatial transcriptomics data☆51Jun 29, 2026Updated 3 weeks ago
- https://sparrow-pipeline.readthedocs.io/en/latest/☆34Updated this week
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆90May 25, 2026Updated last month
- A Snakemake pipeline for Xenium data analysis.☆25Jul 3, 2026Updated 2 weeks ago
- Package for the analysis of Transcripts outside segmented cells in ST data☆30Jul 13, 2026Updated last week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆31Updated this week
- ☆49Apr 8, 2025Updated last year
- ☆100Jul 2, 2026Updated 2 weeks ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆180Updated this week
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆288Updated this week
- ☆32Jan 7, 2026Updated 6 months ago
- Configure Vitessce using existing Scverse plotting APIs☆25Updated this week
- ☆37Jan 22, 2026Updated 5 months ago
- Documentation☆18Feb 25, 2026Updated 4 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.
- ☆23Jun 30, 2026Updated 2 weeks ago
- A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.☆38Jul 7, 2026Updated last week
- Extension of SpatialExperiment with sf☆57May 6, 2026Updated 2 months ago
- List of Spatial Transcriptomics related Tools organized per category☆192Updated this week
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆56Nov 13, 2025Updated 8 months ago
- Compute the neighborhood consolidation matrix and identify SHRs☆14Jun 12, 2025Updated last year
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆111Jun 27, 2026Updated 3 weeks ago
- Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.☆19Sep 19, 2025Updated 10 months ago
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆45Jun 11, 2026Updated last month
- 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.
- An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.☆32Jul 10, 2026Updated last week
- Interoperability between SpatialData and the Xenium Explorer☆26Jul 31, 2024Updated last year
- A multi-dimensional spatial image data structure for scientific Python.☆44Aug 8, 2025Updated 11 months ago
- BANKSY: spatial clustering☆157May 30, 2026Updated last month
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆16Jul 6, 2026Updated 2 weeks ago
- ☆16May 6, 2026Updated 2 months ago
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆71Dec 2, 2025Updated 7 months ago