LEfSe was used to identify differentially abundant features between classes of samples38.
The MACS268 routine bdgdiff was used to identify differentially methylated regions.
The edgeR package (v3.14.0) was then used to identify differentially expressed genes.
To identify differentially expressed genes between control and Nrf2 siRNA-treated samples, DESeq2 algorithm was used50.
Different microarrays were quantile-normalized and a Bayes test used to identify differentially expressed probes.
mirDeep2 (ref. 36) was used to identify differentially expressed miRNAs (DEmiRs) between RA and OA.
Clark, N. et al. The characteristic direction: a geometrical approach to identify differentially expressed genes.
Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes.
To identify differentially expressed genes, we used the Student's t-test and lists were filtered at p ≤ 5%.
The linear model analysis of limma was then used to identify differentially expressed genes between the samples.
To use DNA microarrays to identify differentially expressed genes in eutopic endometrium compared with ectopic endometrium.
