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




On 24.06.19 17:35, Andreas Tille wrote:
Hi,

On Mon, Jun 24, 2019 at 05:24:09PM +0200, Steffen Möller wrote:
I only now learned about
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881317 and the
subsequent removal of r-cran-edger from our distro. Sigh. In that
thread, the discussion about using a wrapper for installing non-free
bits came up. Conda anyone?

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. 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.

Anyway - from what I oversee, the missing edgeR is not critical for bcbio.

Best,

Steffen


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