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Arrays were normalized and differentials were identified with LIMMA (Smyth, 2004) and SAM (Tusher et al., 2001).
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To call differential binding events, samtools rmdup was first used to remove duplicate reads, after which regions of differential enrichment were identified using the MACS2 callpeak and bdgdiff modules.
23 differential metabolites were identified (P < 0.05).
The differential features were identified on the OTU level (relative abundance >1%).
Haplotype blocks that are correlated to differential resistance were identified using the full model linear haplotype trend regression with Bonferroni adjustment.
Single nucleotide polymorphisms (SNPs) associated with differential resistance were identified in the diverse panel and a subset of 198 indica accessions.
Numerous differential reactions were identified among the four cvs in the five Mo populations, suggesting that the Pi gene(s) carried by the donor cv.
A total of 14 differential proteins were identified on 2-DE, whereas label-free quantification resulted in the identification of 1626 non-redundant proteins.
While SVSP transcript levels in different infected cell lines appear to be largely comparable, specific SVSP genes exhibiting differential expression were identified.
Differential genes were identified between each two sets of conditions, and for each set GO functional enrichment was evaluated using TANGO FDR/False Discovery Ratee <0.1) and promoter signals were evaluated using PRIMA (p-value <10−4, uncorrected).
Genes with the most reproducible differential expression were identified by selecting genes in the initial and replication data sets with Log2FC≥1 and P≤0.05, and then assessing the combined statistical significance using the Fisher's combined P method [29].
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