☆31May 21, 2026Updated this week
Alternatives and similar repositories for spatialxe
Users that are interested in spatialxe are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- https://sparrow-pipeline.readthedocs.io/en/latest/☆33Apr 25, 2026Updated 3 weeks ago
- An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.☆15Nov 3, 2025Updated 6 months ago
- Python API and Jupyter widget for Vitessce☆66Apr 17, 2026Updated last month
- Extension of SpatialExperiment with sf☆57May 6, 2026Updated 2 weeks ago
- Compute the neighborhood consolidation matrix and identify SHRs☆14Jun 12, 2025Updated 11 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆90Mar 16, 2026Updated 2 months ago
- FastReseg for detection and correction of cell segmentation error based on spatial profile of transcripts.☆15Apr 30, 2026Updated 3 weeks ago
- BANKSY: spatial clustering☆147May 2, 2026Updated 2 weeks ago
- Integration of gut cell atlases☆35May 6, 2026Updated 2 weeks ago
- Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…☆75May 7, 2026Updated 2 weeks ago
- Accelerated genomics workflows in NextFlow☆41Sep 11, 2024Updated last year
- ☆10May 31, 2022Updated 3 years ago
- ☆95Updated this week
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆277May 7, 2026Updated 2 weeks 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.
- GIve easy, high-level access to ome-zarr fileset☆22Sep 22, 2025Updated 8 months ago
- Single Cell Analysis Operations☆15Nov 25, 2025Updated 5 months ago
- Interactive and integrated analysis of multiplexed tissue microarrays☆15Apr 27, 2026Updated 3 weeks ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆171Updated this week
- Generation of disentangled microenvironment-induced and intrinsic gene expression vectors from spatial transcriptomics data☆26Mar 16, 2026Updated 2 months ago
- Python package to interactively annotate histological images within a jupyter notebook☆18Oct 20, 2025Updated 7 months ago
- An R package for performing cell typing in SMI and other single cell data☆49May 1, 2026Updated 3 weeks ago
- A framework for performing single-cell and bulk read full-length analysis of mutations and splicing.☆63May 6, 2026Updated 2 weeks ago
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆55Nov 13, 2025Updated 6 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Vitessce is a visual integration tool for exploration of spatial single-cell experiments.☆251Updated this week
- A single cell transcriptomics pipeline for QC, integration and making the data presentable☆99Updated this week
- This is a repository of IAMSAM, an image-based ST analysis tool☆22Jun 24, 2025Updated 10 months ago
- Python project containing Ice remoting code for OMERO☆28Apr 22, 2026Updated last month
- An introduction to OME-Zarr for big bioimaging data☆26May 14, 2026Updated last week
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆105Updated this week
- Convert your single-cell/spatial analyses to parallel HPC/cloud workflows just using pipes in R☆18May 14, 2026Updated last week
- An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter☆14Jan 18, 2019Updated 7 years 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 5 months ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Weakly supervised learning uncovers phenotypic signatures in single-cell data☆40Dec 17, 2025Updated 5 months ago
- Bayesian Segmentation of Spatial Transcriptomics Data☆205Apr 30, 2026Updated 3 weeks ago
- A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, i…☆31Mar 14, 2025Updated last year
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆49Jul 16, 2024Updated last year
- Probabilistic pseudotime for single-cell RNA-seq data☆11Oct 6, 2017Updated 8 years ago
- ngio is a Python library to streamline OME-Zarr image analysis workflows.☆49Updated this week
- ☆23Sep 17, 2025Updated 8 months ago