Single cell RNA-seq data clustering using TF-IDF based methods

BMC Genomics
Marmar Moussa, Ion I Măndoiu

Abstract

Single cell transcriptomics is critical for understanding cellular heterogeneity and identification of novel cell types. Leveraging the recent advances in single cell RNA sequencing (scRNA-Seq) technology requires novel unsupervised clustering algorithms that are robust to high levels of technical and biological noise and scale to datasets of millions of cells. We present novel computational approaches for clustering scRNA-seq data based on the Term Frequency - Inverse Document Frequency (TF-IDF) transformation that has been successfully used in the field of text analysis. Empirical experimental results show that TF-IDF methods consistently outperform commonly used scRNA-Seq clustering approaches.

References

Dec 19, 2019·BMC Bioinformatics·Michael HeinzingerBurkhard Rost
Sep 13, 2020·Science Immunology·James T NevinPramod K Srivastava
Sep 26, 2019·Frontiers in Cell and Developmental Biology·Maxwell E R Shafer
Aug 27, 2019·Frontiers in Genetics·Gennaro Gambardella, Diego di Bernardo

Citations

Jan 10, 2003·The Journal of Investigative Dermatology. Symposium Proceedings·Albert M Kligman
Feb 9, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Aaron ClausetCristopher Moore
May 11, 2011·BMC Proceedings·Chih LeeCraig E Nelson
Apr 14, 2015·Nature Biotechnology·Rahul SatijaAviv Regev
Feb 19, 2016·Genome Biology·Tomislav IlicicSarah A Teichmann
Jun 22, 2016·Genome Biology·Brian D OndovAdam M Phillippy
Aug 25, 2016·BMC Genomics·Hung-I Harry ChenYidong Chen
Sep 27, 2016·Cell Metabolism·Åsa SegerstolpeRickard Sandberg
Jan 17, 2017·Nature Communications·Grace X Y ZhengJason H Bielas

Related Concepts

Single-Cell Analysis
Transformation, Genetic
Sequence Determinations, RNA
Sequence Determinations
RNA, Small Cytoplasmic
Gene Expression Profiling
Cell Type
Inhibitory diffusible factor 45
Analysis
Comprehension

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