[Bioc-devel] Announcement of a new package called bacon

[Wolfgang Huber]

There exist people that use Bioconductor devel branch packages even though they are not developers and don’t subscribe to bioc-devel, so I think announcing on the support site can be appropriate.

I understand that problems might arise with & for users who do not easily handle versioning, but IMHO they are more than offset by highlightung a potentially useful package to as many people as possible as early as possible. (I haven’t checked this for a while - does ‘biocLite’ give a useful error message when asked to install a ‘devel only’ package on a system that is set up for release?)

Best wishes
	Wolfgang

> On Jun 9, 2016, at 16:48 GMT+2, Maarten van Iterson <mviterson at gmail.com> wrote:
> 
> So the policy could be: before release to bioc-devel and after release to
> the support-site. Maybe it is more useful to post only on the support-site
> on release? I assume most bioc-devel subscribers follow the support-site.
> 
> Maarten
> 
> On Thu, Jun 9, 2016 at 3:29 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
> 
>> I agree, but bacon is part of release. As Maarten said "
>> *I would like to introduce the package bacon that has been added
>> tobioconductor just before the release of version 3.3." ��*
>> 
>> On Thu, Jun 9, 2016 at 10:09 AM, Martin Morgan <
>> martin.morgan at roswellpark.org> wrote:
>> 
>>> On 06/09/2016 10:06 AM, James W. MacDonald wrote:
>>> 
>>>> You should post this on the support site (
>>>> https://support.bioconductor.org),
>>>> using the 'News' item description. This bioc-devel is intended for
>>>> discussion of issues with development of packages, not really for
>>>> announcing new packages.
>>>> 
>>> 
>>> actually the email to developers on package acceptance encourages them to
>>> post to bioc-devel.
>>> 
>>> I think the rationale was that the package is only available in devel, so
>>> advertising on the support site would just lead to disappointment.
>>> 
>>> Open to revised policies / suggestions, though.
>>> 
>>> Martin
>>> 
>>> 
>>>> Jim
>>>> 
>>>> 
>>>> 
>>>> On Thu, Jun 9, 2016 at 9:37 AM, Maarten van Iterson <mviterson at gmail.com
>>>>> 
>>>> wrote:
>>>> 
>>>> Dear list,
>>>>> 
>>>>> I would like to introduce the package bacon that has been added to
>>>>> bioconductor just before the release of version 3.3.
>>>>> 
>>>>> bacon can be used to estimate and control for bias and inflation often
>>>>> present in epigenome- and transcriptome-wide association
>>>>> studies(EWAS/TWAS). The idea behind bacon is to estimate the empirical
>>>>> null
>>>>> distribution from the data (using Bayesian statistics) and use the
>>>>> empirical null i.s.o. a theoretical null for inference. Bacon supports
>>>>> bias- and inflation-controlled fixed-effect meta-analysis that can be
>>>>> executed in parallel. A manuscript is available from biorxiv (
>>>>> http://biorxiv.org/content/early/2016/05/27/055772).
>>>>> 
>>>>> Kind regards,
>>>>> 
>>>>> Maarten van Iterson
>>>>> 
>>>>>         [[alternative HTML version deleted]]
>>>>> 
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> 
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>> 
>> 
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>> 
> 
> 	[[alternative HTML version deleted]]
> 
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Wolfgang

Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
Genome Biology Unit
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.huber at embl.de
http://www.huber.embl.de