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splatPop: Simulating population scale single-cell RNA sequencing data.
Genome Biol. 22:341 (2021)
Population-scale single-cell RNA sequencing (scRNA-seq) is now viable, enabling finer resolution functional genomics studies and leading to a rush to adapt bulk methods and develop new single-cell-specific methods to perform these studies. Simulations are useful for developing, testing, and benchmarking methods but current scRNA-seq simulation frameworks do not simulate population-scale data with genetic effects. Here, we present splatPop, a model for flexible, reproducible, and well-documented simulation of population-scale scRNA-seq data with known expression quantitative trait loci. splatPop can also simulate complex batch, cell group, and conditional effects between individuals from different cohorts as well as genetically-driven co-expression.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Single-cell Rna-sequencing ; Simulation ; Software; Normalization; Set
ISSN (print) / ISBN
1474-760X
e-ISSN
1465-6906
Journal
Genome Biology
Quellenangaben
Volume: 22,
Issue: 1,
Article Number: 341
Publisher
BioMed Central
Publishing Place
Campus, 4 Crinan St, London N1 9xw, England
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Computational Biology (ICB)
Grants
NHMRC
National Health and Medical Research Council (NHMRC) of Australia
Baker Foundation
National Health and Medical Research Council (NHMRC) of Australia
Baker Foundation