Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
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Cites methods from "Moderated estimation of fold change..."
...Size factors can be computed with several different approaches, e.g., using the estimateSizeFactorsFromMatrix function in the DESeq2 package (Anders & Huber, 2010; Love et al., 2014), or with the calcNormFactors function (Robinson & Oshlack, 2010) in the edgeR package....
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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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"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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