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The dataset provides various information about each peak, including the peak score, the peak center (for STAT1), and the Q-value that reflects the significance of the peak.
Disease maxiumum was delayed, the peak score was significantly reduced (d 22: 2.2±0.5, p<0.001 ***) and the residual score significantly lowered (d 50: 0.8±0.3 (p<0.001 ***; Fig. 1A, Tab. 1).
Thus, based on this algorithm, we wondered what the correlation of octamer motifs (which we will refer to as the OCT4 motif) and the peak score value would be.
These results suggested that the vast majority of HLH-1 bound intervals detected in embryonic chromatin by array hybridizations are factor-specific and are reproducibly detected by deep sequencing or qPCR, with the confidence of detection directly related to the peak score.
The peak score can be calculated using the peak height or read count.
The peak score is then used to determine the point where the read is trimmed.
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The goal is to predict the peak scores from the peak vectors.
PeakRegressor predicts the peak scores and therefore, we have two different values for each peak.
Therefore, using the peak scores lead to better identification of functional TFBMs.
Table 1 shows the correlation coefficients between the peak scores and their predicted values by PeakRegressor in the test dataset.
In contrast with previous approaches, PeakRegressor uses the peak scores (provided by [9]) as a surrogate for the binding affinities.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com