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

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Thu Sep 24 15:01:39 CEST 2020


Others may chime in with their opinions as well but my own thoughts...

I see no reason not to post on the support.bioconductor.org site to request some beta testing users.  I suggest using the "NEWS Event" for post type also explaining / informing of some of the big /extensive changes to the package.  Similarly when the changes are formally released you can post on the support channel but I would either use  "News Event" or "Tutorial" as Post Type rather than a Question.

At release time we do include all changes listed in the NEWS files of packages.  Please make sure the NEWS file is up-to-date and properly formatted and it will also be included there.
Example release announcement from Bioc 3.11 of collated NEWS files:


 If this could potentially impact package that depend, import, suggest your package I might also suggest personally reaching out to those package maintainers to see if they also wanted to beta test and to make sure their packages still function as intended  (I think currently there are two packages based on DiffBind landing page ChIPQC, vulcan)



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Rory Stark <Rory.Stark using cruk.cam.ac.uk>
Sent: Tuesday, September 22, 2020 6:06 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Extensive updates to DiffBind: help reviewing docs and/or beta testing?

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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