DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

By Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang. Bioinform., 2010

4,054 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/d16c72ba11ba9ee16bc65ae6c2917a40541b36d0

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In Molecular Biology

Citations in the corpus

RNA-Seq analysis in MeV (2011, positive): “There are three differential expression analysis methods based on the Bioconductor packages DESeq (Anders and Huber, 2010), DGESeq (Wang et al., 2010) and EdgeR (Robinson et al., 2010) that analyze differential expression using RNA-Seq-specific statistics.”
Computational methods for transcriptome annotation and quantification using RNA-seq (2011, methodology): “, model the count variance across replicates as a nonlinear function of the mean counts using various different parametric approaches (such as the normal and negative binomial distributions”
From RNA-seq reads to differential expression results (2010, methodology): “This has been independently confirmed using a technical experiment [45] and software tools are readily available to perform these analyses [54].”
baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data (2010, methodology): “…and Smyth [9] as implemented in the edgeR [17,18] (version 1.4.7) Bioconductor [19] package, the overdispersed log-linear model of Lu et al [7], the overdispersed logistic model of Baggerly et al [6], and the recently released methods DEGseq [10] (version 1.2.2) and DESeq [11] (version 1.0.4).”
ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq (2013, methodology): “This dataset is often used to evaluate assumptions underlying RNA-Seq methods[23,30] and contains 32000 coding sequences (CDS).”
TCC: an R package for comparing tag count data with robust normalization strategies (2013, background): “Several R [7] packages have been developed for this purpose [8-14].”
Differential analysis of gene regulation at transcript resolution with RNA-seq (2012, methodology): “Current tools for differential gene expression analysis use the raw count method, equating the change in a gene's expression levels with the change in the number of fragments originating from it between conditions 17,20,21,28 .”
Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder (2016, methodology): “The P v a l ue and q v a l ue (29, 30) between samples were generated by DEGseq (31) package of R.”