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Differential Expression was determined using the DESeq version 1.5.6 [ 21].
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Fold-change and differential expression significance values were calculated from gene level read counts using the DESeq package (version 1.8.3) available in Bioconductor (version 2.10).
Differential expression (DE) analysis was performed using the DESeq analysis tool version 1.12.1 (Anders and Huber, 2010).
To test for differential expression between sexes or populations, we used the DESeq package (version 2.10) [ 70] implemented in R (version 2.14.1) [ 71].
Differential expression analysis was performed using the DESeq R package (1.18.0) (Anders and Huber, 2010).
Differential expression analysis of two groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0).
For the DESeq method, differentially expressed genes were detected by using the Deseq R package (1.8.3).
Results were generated using the DESeq 'pooled' method.
Differential analysis using the DESeq 'per condition' method.
Differential expression analysis was performed using the DESeq algorithm.
MiRNA reads were analyzed using the DESeq package [ 31] in R language [ 32].
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