Re: edgeR no longer with us - effect on seqcluster unknown

[Andreas Tille <andreas@an3as.eu>]

On Mon, Jun 24, 2019 at 07:22:54PM +0200, Steffen Möller wrote:
> 
> > > At the very moment I cannot tell about how essential edgeR may be for
> > > seqcluster and the bcbio workflow as a whole - but Debian not offering
> > > that package at all - it is a bit weird.
> > I think what is really weird is the license of locfit (see discussion in
> > #731599) and the fact that it seems impossible to reach locfit upstream.
> Agreed.

> > If you ask me there are chances to talk to CRAN / Bioconductor people
> > that they are relying on non-free software (which is as far as I know
> > also against their polica) but nobody has explained that issue clear
> > enough.  May be its not to hard to create a locfit alternative.
> 
> EdgeR allows locfit to be substituted by other estimators.

At the time when we had the r-bioc-edger package locfit was not
mandatory.  However, I had the feeling that it became default and thus
it was not possible to keep it in main.

> Once I feel
> a bit more mentally superior to it all, I am tempted to suggest a free
> alternative
> to the edgeR developers as a default. But any such scientifically relevant
> change should come from upstream, not as an unsuspected patch within Debian.

Fully agreed - so did you contacted upstream?
 
> Anyway - from what I oversee, the missing edgeR is not critical for bcbio.

I'd love to have it back anyway.

Kind regards

        Andreas. 

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