Literature DB >> 36034329

SAREV: A review on statistical analytics of single-cell RNA sequencing data.

Dorothy Ellis1, Dongyuan Wu1, Susmita Datta1.   

Abstract

Due to the development of next-generation RNA sequencing (NGS) technologies, there has been tremendous progress in research involving determining the role of genomics, transcriptomics and epigenomics in complex biological systems. However, scientists have realized that information obtained using earlier technology, frequently called 'bulk RNA-seq' data, provides information averaged across all the cells present in a tissue. Relatively newly developed single cell (scRNA-seq) technology allows us to provide transcriptomic information at a single-cell resolution. Nevertheless, these high-resolution data have their own complex natures and demand novel statistical data analysis methods to provide effective and highly accurate results on complex biological systems. In this review, we cover many such recently developed statistical methods for researchers wanting to pursue scRNA-seq statistical and computational research as well as scientific research about these existing methods and free software tools available for their generated data. This review is certainly not exhaustive due to page limitations. We have tried to cover the popular methods starting from quality control to the downstream analysis of finding differentially expressed genes and concluding with a brief description of network analysis.

Entities:  

Year:  2021        PMID: 36034329      PMCID: PMC9400796          DOI: 10.1002/wics.1558

Source DB:  PubMed          Journal:  Wiley Interdiscip Rev Comput Stat        ISSN: 1939-0068


  104 in total

1.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Authors:  Evan Z Macosko; Anindita Basu; Rahul Satija; James Nemesh; Karthik Shekhar; Melissa Goldman; Itay Tirosh; Allison R Bialas; Nolan Kamitaki; Emily M Martersteck; John J Trombetta; David A Weitz; Joshua R Sanes; Alex K Shalek; Aviv Regev; Steven A McCarroll
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

2.  dropClust: efficient clustering of ultra-large scRNA-seq data.

Authors:  Debajyoti Sinha; Akhilesh Kumar; Himanshu Kumar; Sanghamitra Bandyopadhyay; Debarka Sengupta
Journal:  Nucleic Acids Res       Date:  2018-04-06       Impact factor: 16.971

3.  FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data.

Authors:  Josip S Herman; Dominic Grün
Journal:  Nat Methods       Date:  2018-04-09       Impact factor: 28.547

Review 4.  Gene regulatory network inference resources: A practical overview.

Authors:  Daniele Mercatelli; Laura Scalambra; Luca Triboli; Forest Ray; Federico M Giorgi
Journal:  Biochim Biophys Acta Gene Regul Mech       Date:  2019-10-31       Impact factor: 4.490

5.  Linnorm: improved statistical analysis for single cell RNA-seq expression data.

Authors:  Shun H Yip; Panwen Wang; Jean-Pierre A Kocher; Pak Chung Sham; Junwen Wang
Journal:  Nucleic Acids Res       Date:  2017-12-15       Impact factor: 16.971

6.  Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures.

Authors:  Thalia E Chan; Michael P H Stumpf; Ann C Babtie
Journal:  Cell Syst       Date:  2017-09-27       Impact factor: 10.304

7.  Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data.

Authors:  Thinh N Tran; Gary D Bader
Journal:  PLoS Comput Biol       Date:  2020-09-09       Impact factor: 4.475

8.  Splatter: simulation of single-cell RNA sequencing data.

Authors:  Luke Zappia; Belinda Phipson; Alicia Oshlack
Journal:  Genome Biol       Date:  2017-09-12       Impact factor: 13.583

9.  SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation.

Authors:  Hirotaka Matsumoto; Hisanori Kiryu; Chikara Furusawa; Minoru S H Ko; Shigeru B H Ko; Norio Gouda; Tetsutaro Hayashi; Itoshi Nikaido
Journal:  Bioinformatics       Date:  2017-08-01       Impact factor: 6.937

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