Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
☆81Oct 28, 2026Updated this week
Alternatives and similar repositories for spatialvi
Users that are interested in spatialvi are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data☆46Updated this week
- ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …☆105Feb 11, 2026Updated 8 months ago
- Spatial One☆32Oct 31, 2024Updated 2 years ago
- Static plotting for spatialdata☆89Oct 19, 2026Updated last week
- ☆20Updated this week
- 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.
- Analysis framework for morphological profiling data☆14Updated this week
- Python API and Jupyter widget for Vitessce☆67Updated this week
- Demultiplexing pipeline for sequencing data☆61Updated this week
- Image Mass Cytometry analysis pipeline☆26Jun 3, 2025Updated last year
- OMERO.web plugin for the Vitessce multimodal data viewer.☆14Jul 29, 2026Updated 3 months ago
- An analysis pipeline for Nanostring nCounter expression data.☆18Updated this week
- A Python package for unsupervised analysis of spatial (prote)omics data.☆19Updated this week
- Spatial transcriptomics of heart tissue☆114Oct 7, 2023Updated 3 years ago
- material related to the genetech courses☆10Sep 11, 2023Updated 3 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- R package implementing affinity propagation clustering along with various utilities☆12Sep 9, 2025Updated last year
- BayesTME: A reference-free Bayesian method for analyzing spatial transcriptomics data☆15Apr 29, 2025Updated last year
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆297Updated this week
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆84Updated this week
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆96Oct 16, 2026Updated 2 weeks ago
- ☆10Oct 7, 2024Updated 2 years ago
- A Bayesian model for compositional single-cell data analysis☆204Jan 13, 2026Updated 9 months ago
- ☆10May 31, 2022Updated 4 years ago
- Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-dropl…☆363Updated this week
- 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.
- ☆32Jan 7, 2026Updated 9 months ago
- Single-cell spatial omics analysis that makes you happy!☆79Updated this week
- Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.☆19Oct 7, 2026Updated 3 weeks ago
- Holoviz Anndata Interface☆14Updated this week
- CODEX data processing code☆13Jul 1, 2025Updated last year
- An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.☆36Updated this week
- Fast array utilities☆15Oct 23, 2026Updated last week
- Workflow for Sequenza, cellularity and ploidy☆28Jun 11, 2026Updated 4 months ago
- A multi-dimensional spatial image data structure for scientific Python.☆45Aug 8, 2025Updated last year
- 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.
- Image registration (alignment) software for large microscopy images☆27Oct 15, 2023Updated 3 years ago
- Interactive visualization of spatial omics data☆91Sep 8, 2026Updated last month
- Bam to Pandas DataFrame, quickly☆13May 10, 2025Updated last year
- Build contrasts for models defined with formulaic☆13Updated this week
- Links between modalities in mudata☆17Oct 16, 2026Updated 2 weeks ago
- Multimodal Data (.h5mu) implementation for Python☆134Updated this week
- A collection of project templates and useful functions for single-cell data analysis with Scanpy.☆22Jun 12, 2023Updated 3 years ago