Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis

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 syste...

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Bibliographic Details
Published in:Genome Biology Vol. 25; no. 1; p. 181
Main Authors: Curion, Fabiola, Rich-Griffin, Charlotte, Agarwal, Devika, Ouologuem, Sarah, Rue-Albrecht, Kevin, May, Lilly, Garcia, Giulia E. L., Heumos, Lukas, Thomas, Tom, Lason, Wojciech, Sims, David, Theis, Fabian J., Dendrou, Calliope A.
Format: Journal Article
Language:English
Published: London BioMed Central 08.07.2024
Springer Nature B.V
BMC
Subjects:
Animal Genetics and Genomics
Automation
Best practice
Bioinformatics
Biomedical and Life Sciences
Clustering
Data analysis
data collection
Datasets
Decision making
epigenome
Evolutionary Biology
Gene Expression Profiling - methods
Genomics
Human Genetics
Humans
Life Sciences
Metadata
Microbial Genetics and Genomics
Plant Genetics and Genomics
proteome
Proteomes
Quality control
Sensory integration
Single-Cell Analysis - methods
Software
Transcriptome
Transcriptomes
Transcriptomics
Workflow
ISSN:1474-760X, 1474-7596, 1474-760X
Online Access:Get full text
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Summary: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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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-024-03322-7