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This method only counts viable phages that are able to infect and lyse their host.
During this period, more than one infection might have occurred in one individual, whereas our method only counts one.
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Furthermore, how to accurately quantify the expression of circRNAs is still a challenge since existing methods only count the junction reads, which are easily affected by multiple factors such as sequencing depth, read length, and fragmentation condition during RNA-seq library construction.
These methods only count one sequence per transcript hence will not suffer from transcript length effects.
When quantifying productivity losses, we will use the friction-cost method, which only counts productivity loss for the time it takes to replace a worker.
Our reconstruction method is one such method since our distance estimator only counts the number of shared adjacencies between genomes and the number of linear chromosomes in each of them.
Second, the counting method only cares about whether the local decision consists with the final decision or not.
With the MIL3D method, there are 11 TFs with AUCs above 0.95, while with the 5-mer counting method, only has 2 TFs (Foxo4 and Gmeb2) have AUCs greater than 0.95.
Several additional comments: The authors state in the methods that "we only counted single nucleotide substations".
Only counts and frequencies of the methods used in the sampled literature were used in the analysis.
Automatically and manually detected spines were compared on a spine-by-spine basis and the counts for both methods, for the manual method only, or for NeuronStudio only, were tabulated for each stack (Table 1).
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