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Then, mapping coordinates of orphaned reads along with various SAM fields were extracted and used as an input to insertion site scoring scheme for significant cluster detection.
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A flux diagram summarizing how it works can be seen in Fig. 4. OSLOM consists of three phases: First, it looks for significant clusters, until convergence; Second, it analyzes the resulting set of clusters, trying to detect their internal structure or possible unions thereof; Third, it detects the hierarchical structure of the clusters.
We thus developed the StretchFinder algorithm that tests for significant clustering of consecutive conserved codon sites.
These methods use different approaches (semi-parametric to parametric) to test for significant clusters.
The first of the two algorithms tested for significant clustering of births.
We took a threshold of cluster-wise p values of 0.05 as the criterion for significant clusters.
Maximum χ is a substitution distribution method that searches for significant clustering of substitutions at putative recombination break points (Maynard Smith 1992).
As a third example, we used WordCluster to search for significant clusters of olfactory receptor (OR) genes, the largest multigene family in multicellular organisms whose members are known to be clustered within vertebrate genomes [ 18, 19].
Non-parametric MANOVA were conducted in R [ 45] using the 'adonis' command line in the 'vegan' package [ 46], in order to test for significant clustering of different dietary guilds and of taxonomic orders within the morphospace.
For each significant cluster, we extracted mean activation values for each participant averaged across the active voxels using the MarsBaR toolbox (http://marsbar.sourceforge.net/).net/
Based on this significance criterion, the empirically determined cluster size for each significant cluster is reported in Table 2. Within the clusters that showed two-tailed family-wise error-corrected significant differences between groups, we calculated the mean value of the DTI measure across all voxels within the cluster for each subject.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com