ArticleGigaScience2022
Spacemake: processing and analysis of large-scale spatial transcriptomics data.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Article
- Mapping Embryonic Mouse Lung Development Using Enhanced Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Trustworthy Agentic AI in Bioinformatics: From Workflow Automation to Traceable and Validated Biological Inference.Biology · 2026Review
- stPipe: a flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data.NAR genomics and bioinformatics · 2025Article
- Modular, open-sourced multiplexing for democratizing spatial omics.Lab on a chip · 2025Article
- Fast analysis of Spatial Transcriptomics (FaST): an ultra lightweight and fast pipeline for the analysis of high resolution spatial transcriptomics.NAR genomics and bioinformatics · 2025Article
- Protocol for high-resolution 3D spatial transcriptomics using Open-ST.STAR protocols · 2025Article
- Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments.Bioinformatics (Oxford, England) · 2024Article
- Next-generation spatial transcriptomics: unleashing the power to gear up translational oncology.MedComm · 2024Review
- SpatialOne: end-to-end analysis of visium data at scale.Bioinformatics (Oxford, England) · 2024Article
- GNTD: reconstructing spatial transcriptomes with graph-guided neural tensor decomposition informed by spatial and functional relations.Nature communications · 2023Article
- Establishment and application of TSDPSO-SVM model combined with multi-dimensional feature fusion method in the identification of fracture-related infection.Scientific reports · 2023Article
- Spatiotemporal, optogenetic control of gene expression in organoids.Nature methods · 2023Article
- A unified pipeline for FISH spatial transcriptomics.Cell genomics · 2023Article
- Article
- Spatial transcriptomics in glioblastoma: is knowing the right zip code the key to the next therapeutic breakthrough?Frontiers in oncology · 2023Review
- Article
- Optocoder: computational decoding of spatially indexed bead arrays.NAR genomics and bioinformatics · 2022Article
- Spatial components of molecular tissue biology.Nature biotechnology · 2022Review
- Spatial transcriptomics technology in cancer research.Frontiers in oncology · 2022Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSpatial sequencing methods increasingly gain popularity within RNA biology studies. State-of-the-art techniques quantify messenger RNA expression levels from tissue sections and at the same time register information about the original locations of the molecules in the tissue. The resulting data sets are processed and analyzed by accompanying software that, however, is incompatible across inputs from different technologies.
findingsHere, we present spacemake, a modular, robust, and scalable spatial transcriptomics pipeline built in Snakemake and Python. Spacemake is designed to handle all major spatial transcriptomics data sets and can be readily configured for other technologies. It can process and analyze several samples in parallel, even if they stem from different experimental methods. Spacemake's unified framework enables reproducible data processing from raw sequencing data to automatically generated downstream analysis reports. Spacemake is built with a modular design and offers additional functionality such as sample merging, saturation analysis, and analysis of long reads as separate modules. Moreover, spacemake employs novoSpaRc to integrate spatial and single-cell transcriptomics data, resulting in increased gene counts for the spatial data set. Spacemake is open source and extendable, and it can be seamlessly integrated with existing computational workflows.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.