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The MET module takes methylation calls generated from the bisulfite aligner such as BS Seeker 2, and gene annotation file for analyses.
The patient identifiers were replaced using a de-identification cross-walk to a unique study ID and then all data were imported into a single analytical file for analyses.
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An overview of the InforSense architecture and workflow methodology, used in preparing the data files for analyses are shown in Figure 1.
The DVR Live Capture computer program (Novus Security, 2009, Warsaw, Poland) controlled the cameras and saved the video files for analyses.
All study data were entered in an Access database and converted to files for analyses using Statistical Package for Social Sciences version 19.0 software.
It is therefore recommended that if a user wishes to use specific annotation files for analyses, it is first worth checking with the provider of the file to determine if there are any significant changes to the datasets that should be considered.
We constructed a phylogeny of all species (Fig 2, see additional file 5[ 45]) for analyses of the relationship between mutation rate and extra-pair paternity, while simultaneously considering similarity in phenotype among species due to common phylogenetic descent.
In each study, researchers examined a unique index test, making direct comparisons of index tests and collection of summary statistics impossible (see Additional file 3 for analyses that were planned).
We chose to use temperature and salinity at spawning time (but see also additional file 3 for analyses applying a wider set of closely related environmental variables) since this is as close as possible to the most critical time of the cod life-cycle, i.e. when the life stages (i.e. egg and larvae) have little option for actively avoiding unfavourable conditions (see also discussion in [ 61]).
Finally, GeneLink maintains a list of previously exported files, which eliminates redundant generation of data files by collaborators and functions as an archive of data files used for analyses.
Export data as CSV file for further analyses.
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