Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
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Cites background from "Moderated estimation of fold change..."
...Supplementary Materials: Materials and Methods Figures S1-S59 Tables S1-S43 External Databases S1-S6 15 References (54-184)...
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...S1 to S59 Tables S1 to S43 References (56–186) Databases S1 to S5 13 December 2017; accepted 11 July 2018 10.1126/science.aar7191 International Wheat Genome Sequencing Consortium (IWGSC), Science 361, eaar7191 (2018) 17 August 2018 13 of 13...
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Cites methods from "Moderated estimation of fold change..."
...To identify differentially-expressed genes between the CD69+ and CD69-sorted populations, we used DESeq288 and filtered for significant genes with a log2-fold change in expression greater than 1.5 and a q-value of less than 0.0189....
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...To identify differentially-expressed genes between the CD69+ and CD69- sorted populations, we used DESeq2 [Love et al., 2014] and filtered for significant genes with a log2-fold change in expression greater than 1....
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"Moderated estimation of fold change..." refers methods in this paper
...TheWald test P values from the subset of genes that pass an independent filtering step, described in the next section, are adjusted for multiple testing using the procedure of Benjamini and Hochberg [21]....
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...The Wald test p-values from the subset of genes that pass an independent filtering step, described in the next section, are adjusted for multiple testing using the procedure of Benjamini and Hochberg [20]....
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...For all algorithms returning P values, the P values from genes with non-zero sum of read counts across samples were adjusted using the Benjamini–Hochberg procedure [21]....
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...TheWald test P values from the subset of genes that pass the independent filtering step are adjusted for multiple testing using the procedure of Benjamini and Hochberg [21]....
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...The Wald test p-values from the subset of genes which pass the independent filtering step are adjusted for multiple testing using the procedure of Benjamini and Hochberg [20]....
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29,413 citations
"Moderated estimation of fold change..." refers methods in this paper
...The Negative Binomial based approaches compared were DESeq (old) [4], edgeR [32], edgeR with the robust option [33], DSS [6] and EBSeq [34]....
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