See also the official documentation - MethylKit Vignette
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https://github.com/sr320/paper-oly-mbdbs-gen/blob/master/code/01-methylkit.Rmd - used to processes BS-MBDSeq Data from Olympia oysters, run on personal computer (not Mox). Author: Laura Spencer
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https://github.com/hputnam/Meth_Compare/blob/master/code/MethCompare_methylKit_analysis.R coral methylation comparison of methods.
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https://github.com/epigeneticstoocean/paper-gonad-meth/blob/master/code/04-methylkit.Rmd eastern oyster OA work
Flowchart of possible operations by methylKit. A summary of the most importantmethylKit features is shown in a flow chart. It depicts the main features of methylKitand the sequential relationship between them. The functions that could be used for thosefeatures are also printed in the boxes. - Figure and caption from Akalin et al. 2012