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Sanger sequencing data was also assembled using SeqMan Pro 8.1.1, using the default parameters recommended, that thus allowed us to perform joint 454-Sanger assemblies.
These differentially expressed sets were used as input to the DAVID tool using the default parameters recommended by the developers.
Our goal was to provide an initial overview of methods using the default settings recommended; it should be noted that each dataset must be treated uniquely and alternative parameter settings may deliver more accurate results.
Data were normalized using the default normalization method recommended by the GeneSpring software.
Activity-based estrus alerts were initially identified using the default activity threshold value recommended by the manufacturer, but a range of activity threshold values was then analyzed to determine their effect on estrus detection performance.
For each assembler, we used the default parameters recommended for transcriptome assembly.
For each assembler, we used the default parameters recommended for transcriptome assembly (details are given in Methods).
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The recommended procedure consist in first run the algorithm using the default configuration, correcting afterwards those weights needed to reach the desired results in terms of the objectives.
By default, we recommend to use a broad spectrum of aggressiveness using the default values 0.5· n par < dim_ refset < 20· n par ; 0 < local.n2 < 100; 0 < balance < 0.5; and 5· n par < ndiverse < 20· n par. Figure 2 shows the cooperative loop, and Algorithm 2 summarizes its pseudo-code.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.
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CEO of Professional Science Editing for Scientists @ prosciediting.com