Motivation
Single-cell RNA sequencing (scRNA-seq) enables transcriptome-wide gene expression measurements at single-cell resolution providing a comprehensive view of the compositions and dynamics of tissue and organism development. The evolution of scRNA-seq protocols has led to a dramatic increase of cells throughput, exacerbating many of the computational and statistical issues that previously arose for bulk sequencing. In particular, with scRNA-seq data all the analyses steps, including normalization, have become computationally intensive, both in terms of memory usage and computational time. In this perspective, new accurate methods able to scale efficiently are desirable.
Results
Here we propose PsiNorm, a between-sample normalization method based on the power-law Pareto distribution parameter estimate. Here we show that the Pareto distribution well resembles scRNA-seq data, especially those coming from platforms that employ unique molecular identifiers (UMIs). Motivated by this result, we implement PsiNorm, a simple and highly scalable normalization method. We benchmark PsiNorm against seven other methods in terms of cluster identification, concordance and computational resources required. We demonstrate that PsiNorm is among the top performing methods showing a good trade-off between accuracy and scalability. Moreover PsiNorm does not need a reference, a characteristic that makes it useful in supervised classification settings, in which new out-of-sample data need to be normalized.
Availability
PsiNorm is implemented in the scone Bioconductor package and available at https://bioconductor.org/packages/scone/
Supplementary information
Supplementary data are available at Bioinformatics online.
These study data seem to confirm our hypothesis that plate fixation for DHFs guarantees adequate fracture osteosynthesis and satisfactory functional outcomes at medium to long-term follow-up, not only in elderly patients, but also in octogenarian osteoporotic patients (≥85 years) with 13-C1 and 13-C2 fracture patterns, while an alternative solution should be considered for type C3 fractures, even in a primary trauma setting.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.