A statistical method for detecting differentially expressed SNVs based on next-generation RNA-seq data

DOI10.1111/BIOM.12548MaRDI QIDQ5347401zbMATH OpenOpenAlexWikidataFDO

Authors

Publication date 23 May 2017

Published in Biometrics (Search for Journal in Brave)

Full work available at URL http://europepmc.org/articles/pmc5151178

zbMATH Keywords

differential expressionRNA-seqlikelihood ratio teststatistical methodallele-specific expressionbreast cancer tumors

Mathematics Subject Classification ID

Parametric hypothesis testing (62F03) Applications of statistics to biology and medical sciences; meta analysis (62P10) Protein sequences, DNA sequences (92D20)

Recommendations

• Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates
• Modifying SAMseq to account for asymmetry in the distribution of effect sizes when identifying differentially expressed genes
• Modeling the next generation sequencing read count data for DNA copy number variant study
• Single-sample SNP detection by empirical Bayes method using next-generation sequencing data
• Outlier sums for differential gene expression analysis

Cites work

• scientific article; zbMATH DE number 720689 (Why is no real title available?)
• A penalized EM algorithm incorporating missing data mechanism for Gaussian parameter estimation

Cited in

(4)

• Zero-Inflated Poisson Models with Measurement Error in the Response
• Single-sample SNP detection by empirical Bayes method using next-generation sequencing data
• Analysis of expression profile and gene variation via development of methods for next generation sequencing data
• abSNP: RNA-Seq SNP calling in repetitive regions via abundance estimation

Describes a project that uses

Uses Software

• GATK
• DEseq
• STAR

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