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@nmclark2 nmclark2 released this 06 Apr 15:02
· 41 commits to master since this release
v3.0
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Learn about vigilant mode.

  • Known compatibility: R 3.6.3, R 4.1.3

  • Packages are now automatically installed and loaded using the pacman package.

  • Cluster expression is no longer automatically plotted, and the "Cluster Plots" folder is no longer automatically generated. This is to reduce the runtime of the clustering methods. Cluster expression plots can still be generated by uncommenting the plotting code in the ica_clustering.R (non-temporal) and/or dtw_clustering.R (temporal) files.

  • The help text present in the RShiny App Window is now also included as a .html vignette file.

  • Fixes multiple issues with network inference including adding checks for enough regulators/targets when using clustering and dealing with PTM information in regulator names. We recommend users denote PTM sites in regulator names using a "." (e.g. SOX2.S35) as this is a character not usually present in gene symbols, making it easy to separate the PTM site from the gene name if desired in downstream processing.

  • Networks are no longer trimmed automatically. Rather, the user chooses an edge weight cutoff to use for trimming. For more details, see the vignette.

  • Changes definition of the clustering threshold for non-temporal clustering. For more details, see the vignette.

  • Using the arrows on the edge weight or clustering thresholds will increment by 0.1. NOTE: There is a known issue on MacOS where the arrows will increment by twice the desired step size (e.g. 0.2 instead of 0.1). The user can always specify an exact number by typing it into the box.

  • Adds a button which will save a screenshot of the window to the working directory.

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