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A total of 349 ER+ luminal tumors from the TCGA dataset were ranked from high to low PTEN mRNA levels (log2 transformed and median-centered).
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Similar to the analysis shown in Figure 3, co-expressed gene pairs for each dataset were ranked according to distances calculated from one, two, or three species and each ranked list was evaluated using GO and KEGG functional annotation.
The 18,023 genes form the expression dataset were ranked by level of expression (from lowest to highest) in FC compared to naïve controls and plotted against the average coverage of H4K5ac ± 5 kb relative to the TSS.
Genes from our dataset were ranked by their average fold difference in expression between OSE to CEPI.
Samples from the Frankfurt dataset were ranked according to visual inspection of the amount of stained lymphocytes with the respective antibody in a blinded analysis.
The genes in each dataset were ranked and scored using the methods described.
Genes whose expression correlated with REGγ in each dataset were ranked based on their p-value.
The combined human and mouse dataset was ranked by distance from each sample (Manhattan, Euclidean, or Spearman correlation).
The drug dataset was ranked most structurally diverse, followed by marine and plant derived NPs, respectively.
In contrast, no significant enrichment was observed when the dataset was ranked according to EGFR status.
In brief, accuracies from the six methods were ranked from the highest to the lowest in each of the fourteen datasets.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com