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.
Cheers-
Rory
[[alternative HTML version deleted]]
_______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
