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We encourage you to use this frame work to explore your own data and hope that you will add it to the public repository as well. If you have any problems adding your own data or with the exisiting data, please contact us . The following are the basic steps to add data.

This takes in the resulting output of JTK Cycle . For more information on the parameters used to process data with JTK Cycle, please refer to XXX (preprint/pub). The resulting .txt files are then further processed in Step 2.

Your sampling frequencing and headers may differ from ours. So you can alter your naming scheme to match ours, (if it makes sense to) or you might need to replace your data with ours. Replacing our data with yours is a bit more involved, because, it will change the header names for the graphing steps downstream. For now we will assume that your data headers are like ours. There is a R script in the data folder called setaria-circadian.R. The setaria-circadian.R script was used to add some additional information to the JTK Cycle output. For example, two JTK Cycle outputs were joined together with an rbind step then merged with an annotation file. We add in columns for species name, categories for BH.Q and ADJ.P, and then find the maximum expression value per replicate so that normalized data can be calculated. Once all of these things are done, we have have the raw (expression values not normalized to maximum) and relative/normalized expression data tables that are used as input data. Once you add the necessary columns your dataset, you could rbind it to to the Setaria dataset and reload the app.

There is a file called entrainment.information.txt. Add a row to that file with your sample information and save it.