Cerebro v1.2.2

Bump to Cerebro v1.2.2.

Please refer to the changelog on the cerebroApp website for an explanation of the changes to the Cerebro user interface.

Specific to the standalone version of Cerebro is the implementation of portfinder, which is used to host the internal Shiny app on an open port rather than a fixed port. This should avoid problem when launching Cerebro shortly after a previous instance was closed. Moreover, the Electron framework was updated to v9 to fix (in this case likely harmless) security warnings.

Due to increasing incompatibilities between the old R version inside the standalone version of Cerebro and the dependencies of the cerebroApp R package, this is the most recent version of Cerebro that I can currently bottle into a standalone version.

Cerebro v1.1.0

This release is a substantial update, including functionality to visualise trajectories calculated with Monocle 2 and perform gene set enrichment analysis for samples and clusters using the GSVA method.

Due to internal modifications of the Cerebro object, Cerebro files (.crb) are not backwards-compatible and need to be generated using the export function of cerebroApp v1.1.0. Moreover, pathway enrichment analysis with Enrichr should be re-run to make sure the results are stored in the right format. Alternatively, Cerebro files generated with cerebroApp v1.0 can still be visualised in Cerebro v1.0. We apologise for the inconvenience but decided to proceed in this direction to make it easier to implement features in the future.

Cerebro v1.0

Release that goes along the article submission on bioRxiv: https://www.biorxiv.org/content/10.1101/631705v1