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Then we pooled together data from different networks, and built one 2×2 table for each genus: rows contained the count of modules that followed our prediction and the count of modules that did not; columns contained observed and expected values (equal proportions).
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These were identified by a combination of PILER-CR 1.02, CRT 1.1 and manual correction using BLASTN leading to slightly higher counts of repeat/spacer modules than previously published for strains 4a L99 and 1/2a EGD-e [ 21, 68, 69] (Additional file 8).
We therefore scored genes for type 2 diabetes coexpression by counting the number of modules they appeared in.
While for the former method we just counted the number of modules each time a maximum for the modularity function was obtained, for the latter method we kept the length of the RW to default values, thus allowing for module merging to be as much informative as possible (i.e. neither too stringent nor too conservative in considering the most relevant modules).
It would surely count toward completion of Module 19, which emphasized empathy for the dispossessed.
At the end of the output file, the total number of entries classified by REPCLASS, and the breakdown of this count by module or combination of modules, is given.
To compare different results with approximately the same number of modules, we count the number of GO terms enriched in the modules at a given significance level.
'Touch count' module of iTEM software was used to quantify (i) number of gold particles and (ii) number of grid nodes inside the lysosome profile.
The 'Touch count' module of the iTEM software was utilized to count the number of lipofuscin granules in the 25 μm areas distributed randomly across the RPE layer.
The 'Touch count' module of the iTEM software was used to count the number of lipofuscin granules in 25 µm areas (at least 40) distributed randomly across the RPE layer.
Briefly, the 'Touch count' module of the iTEM software was used to count the number of gold particles per cilium that were then normalized to the cilium perimeter (nm) measured using the 'Closed polygon tool'.
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