Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
☆75May 7, 2026Updated last month
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:
- ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …☆99Feb 11, 2026Updated 4 months ago
- Static plotting for spatialdata☆82Updated this week
- A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data☆31May 31, 2026Updated last week
- Spatial transcriptomics of heart tissue☆111Oct 7, 2023Updated 2 years ago
- Image Mass Cytometry analysis pipeline☆26Jun 3, 2025Updated last year
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Spatial One☆30Oct 31, 2024Updated last year
- Python API and Jupyter widget for Vitessce☆67Jun 4, 2026Updated last week
- An analysis pipeline for Nanostring nCounter expression data.☆18Apr 30, 2026Updated last month
- An introduction to OME-Zarr for big bioimaging data☆27Jun 2, 2026Updated last week
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆44May 27, 2026Updated 2 weeks ago
- Workflow for Sequenza, cellularity and ploidy☆28Jun 1, 2026Updated last week
- Single-cell spatial omics analysis that makes you happy!☆65Updated this week
- Demultiplexing pipeline for sequencing data☆54May 11, 2026Updated last month
- A multi-dimensional spatial image data structure for scientific Python.☆44Aug 8, 2025Updated 10 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.
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆94May 29, 2026Updated 2 weeks ago
- Build contrasts for models defined with formulaic☆13Updated this week
- A Bayesian model for compositional single-cell data analysis☆198Jan 13, 2026Updated 4 months ago
- Bioinformatics web-platform visualisation dashboard creation☆44Jun 5, 2026Updated last week
- Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.☆18Jun 3, 2025Updated last year
- A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)☆13Apr 30, 2026Updated last month
- ☆10May 31, 2022Updated 4 years ago
- Image registration (alignment) software for large microscopy images☆27Oct 15, 2023Updated 2 years ago
- Automatically source dotenv files into your Nextflow scope☆10Mar 27, 2026Updated 2 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.
- Bam to Pandas DataFrame, quickly☆13May 10, 2025Updated last year
- Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-dropl…☆330Updated this week
- scRNA-seq Shiny App☆14May 1, 2023Updated 3 years ago
- Test genes for Spatial Variation☆15Dec 20, 2024Updated last year
- ☆15Apr 7, 2026Updated 2 months ago
- BayesTME: A reference-free Bayesian method for analyzing spatial transcriptomics data☆14Apr 29, 2025Updated last year
- Differential gene expression analysis and pathway analysis of RNAseq data☆32Jul 3, 2025Updated 11 months ago
- Nextflow plugin implementation skeleton☆11Sep 1, 2025Updated 9 months ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆280Jun 1, 2026Updated last 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.
- scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data☆32Dec 22, 2022Updated 3 years ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆87Nov 16, 2025Updated 6 months ago
- Pipeline for SpatialTranscriptomics and 10X Visium data☆22Jul 22, 2025Updated 10 months ago
- Nextflow pipeline wrapper for executing Cell Ranger☆13Mar 8, 2022Updated 4 years ago
- Interactive visualization of spatial omics data☆86May 15, 2026Updated 3 weeks ago
- Access nextflow variables from python scripts or notebooks☆20Apr 11, 2021Updated 5 years ago
- marker-based purification of cell types from single-cell RNA-seq datasets☆141Mar 13, 2026Updated 2 months ago