[Bioc-devel] Extensive updates to DiffBind: help reviewing docs and/or beta testing?

Rory Stark Rory@St@rk @end|ng |rom cruk@c@m@@c@uk
Wed Sep 23 00:06:44 CEST 2020

I've checked in extensive updates to the DiffBind ChIP/ATAC analysis package to reflect current best practices. I'm looking for help/advice in the following areas:

  1.  Reviewing the documentation (particularly the updated vignette), and/or beta-testing the code by running analyses on real data, if anyone on this list is interested. Is there any reason I shouldn't also make this request in the form of a question on the Bioconductor support forum?
  2.  Advice regarding the best way to inform users of the updates when the package is released next month. I don't really see announcements of package updates in any specific place. Is it appropriate to post it as a "question" on the support site, or is there a better forum?

The main updates are in the areas of modelling (full generalized designs and contrasts enabled), analysis (more standardized use of the underlying edgeR and DESeq2 packages), normalization (many new options, including background, offsets, and spike-ins, with an extended vignette section on this topic), and the automatic application of blacklists (and generation of experiment-specific greylists from control reads).

Feel free to contact me directly with questions/comments regarding the package.


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