I started playing around with CAGEr, but following the vignette (v1.33.1, March 19th 2021) I see the vignette si centred around CAGEexp objects but several functions seem to not be implemented for CAGEexp objects yet, and only work for CAGEset.

I'm moving to CAGEset, but I was wondering about the reason for the change from CAGEset to CAGEexp.

• Is it due to any issue that would be good to be aware of before getting knee-deep into pipeline setup?
• Is there any plan to release a new version completing the transition to CAGEexp or will the current one will be the final version of the package for the next future?

PS I'm not sure if there's a version name mistake but the vignette says 1.33.1 while on bioconductor the last available one is 1.32.1

Hi, we are preparing a version 2.0 of CAGEr in which CAGEset is removed and the extra-G removal and promoter shift functions are finally re-implemented. You can follow our progress on GitHub and in the devel branch of Bioconductor.