A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
☆70Apr 24, 2026Updated last month
Alternatives and similar repositories for webatlas-pipeline
Users that are interested in webatlas-pipeline are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.☆15Nov 3, 2025Updated 7 months ago
- Basic example of using OME-Zarr in a Nextflow pipeline☆21Jul 15, 2025Updated 11 months ago
- A probabilistic cell typing algorithm for spatial transcriptomics.☆26May 26, 2026Updated 3 weeks ago
- Vitessce is a visual integration tool for exploration of spatial single-cell experiments.☆254Updated this week
- A variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics☆13Mar 11, 2024Updated 2 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.
- CeLEry: cell location recovery in single-cell RNA sequencing☆38Feb 14, 2025Updated last year
- Create web-based OME-Zarr galleries☆25May 26, 2026Updated 3 weeks ago
- Package for the analysis of Transcripts outside segmented cells in ST data☆30Updated this week
- ☆40Jun 24, 2025Updated 11 months ago
- Python package to interactively annotate histological images within a jupyter notebook☆18Oct 20, 2025Updated 7 months ago
- Multi-omic single-cell optimal transport tools☆212Jun 11, 2026Updated last week
- Raw format to OME-TIFF converter☆57Apr 24, 2026Updated last month
- ☆16Sep 29, 2023Updated 2 years ago
- https://sparrow-pipeline.readthedocs.io/en/latest/☆33Updated this week
- 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.
- ☆13Jul 1, 2021Updated 4 years ago
- Spatial reconstruction of dissociated single-cell data☆20Jan 12, 2024Updated 2 years ago
- Comprehensive pipeline for donor demultiplexing in single cell☆26May 17, 2026Updated last month
- ☆30Oct 4, 2024Updated last year
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆87Nov 16, 2025Updated 7 months ago
- Minimum Information about Tissue Imaging☆21Oct 18, 2023Updated 2 years ago
- End-to-end pipeline for segmenting cell nuclei on histology slides☆16Jul 19, 2022Updated 3 years ago
- Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology☆132May 29, 2025Updated last year
- Spot pseudo-Imager on top of histology☆50Dec 12, 2025Updated 6 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆280Updated this week
- Spatial Single-Cell Analysis Toolkit☆112Mar 11, 2026Updated 3 months ago
- WebGL-based viewer for spatially-resolved transcriptomics data☆28Jan 6, 2023Updated 3 years ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆175May 18, 2026Updated last month
- CAST package☆44Oct 26, 2024Updated last year
- Cell level integrated analysis of tissue histology and spatial transcriptomics☆32Oct 6, 2025Updated 8 months ago
- ☆34Jun 8, 2026Updated last week
- Probabilistic Alignment of Spatial Transcriptomics Experiments v.2☆42Mar 2, 2025Updated last year
- Analysis of imbalanced data and its impacts in a scRNA-seq integration setting☆31Mar 7, 2025Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- cell type specific, trait-associated gene regulation☆30Mar 31, 2025Updated last year
- cell type deconvolution for multi-condition bulk RNA-seq data☆33Feb 28, 2022Updated 4 years ago
- Trends in single cell papers☆17Sep 23, 2024Updated last year
- ☆12May 29, 2024Updated 2 years ago
- Pydantic models for OME-NGFF☆24Sep 14, 2025Updated 9 months ago
- Convert Seurat objects to 10x Genomics Loupe files.☆155Apr 24, 2026Updated last month
- Fast reconstruction of spatial networks from bioimages.☆26Mar 27, 2026Updated 2 months ago