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We thank Hee Shin Kim, Ajith Harish, Minglei Wang, and Jay E. Mittenthal for helpful discussions, and Minglei Wang for scripts to calculate node distances.
JL wrote scripts to calculate land-cover types around homes.
Data analysis was accomplished with SQL scripts to calculate average and standard deviation for each transcript.
Then we used the scoring scripts to calculate one c-index.
We then used Perl scripts to calculate gene length, protein length, number of exons, and GC content of the genes.
Samtools was also used with in-house scripts to calculate coverage estimates and to compare frequencies between the groups.
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We wrote a short computer script to calculate nucleotide frequencies.
The above scripts from Bisognin et al. were used by an additional script to calculate the number of genomic clusters for 1000 randomly generated lists of 675 probesets [53].
ANOVA for the probe sets that passed these filters was done with a Visual Basic script to calculate F ratios, which were exported to a Microsoft Excel spreadsheet for determination of nominal P values.
We then used a custom script to calculate CDS ranges within the chromosome files.
We used a custom python script to calculate the ortholog hit ratio.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com