ArticleGenome biology2024
Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
12 citing papers in PubMed.
- Integrating Spatial Proteogenomics in Cancer Research.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- CERTOMICS: trusted single-cell multiomics pipeline for high-resolution profiling of adoptive cellular immunotherapies.Bioinformatics (Oxford, England) · 2026Article
- Multimodal artificial intelligence and machine learning in oncology: from data integration to precision cancer care.Frontiers in digital health · 2026Review
- Early lymph node T follicular helper cell signalling hub drives influenza vaccine response in an ancestrally diverse cohort.EBioMedicine · 2025Article
- Modular, open-sourced multiplexing for democratizing spatial omics.Lab on a chip · 2025Article
- Ex vivo model of functioning human lymph node reveals role for innate lymphocytes and stroma in response to vaccine adjuvant.Cell reports · 2025Article
- Single-cell genomics and spatial transcriptomics in islet transplantation for diabetes treatment: advancing towards personalized therapies.Frontiers in immunology · 2025Review
- Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis.Genome biology · 2024Article
- Leveraging Multi-Tissue, Single-Cell Atlases as Tools to Elucidate Shared Mechanisms of Immune-Mediated Inflammatory Diseases.Biomedicines · 2024Review
- hadge: a comprehensive pipeline for donor deconvolution in single-cell studies.Genome biology · 2024Article
- Scaling up single-cell RNA-seq data analysis with CellBridge workflow.Bioinformatics (Oxford, England) · 2023Article
- CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data.Journal of visualized experiments : JoVE · 2023Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
Single-cell multiomic analysis of the epigenome, transcriptome, and proteome allows for comprehensive characterization of the molecular circuitry that underpins cell identity and state. However, the holistic interpretation of such datasets presents a challenge given a paucity of approaches for systematic, joint evaluation of different modalities. Here, we present Panpipes, a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale. Panpipes allows reliable and customizable analysis and evaluation of individual and integrated modalities, thereby empowering decision-making before downstream investigations.
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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.