Subject: ITP: rosa -- Removal of Spurious Antisense in biological RNA sequences
Package: wnpp
Owner: Steffen Moeller <moeller@debian.org>
Severity: wishlist

* Package name    : rosa
  Version         : 1.0
  Upstream Author : University of Dundee, UK
* URL             : https://github.com/bartongroup/RoSA
* License         : GPL-3.0+
  Programming Lang: Python
  Description     : Removal of Spurious Antisense in biological RNA sequences
 In stranded RNA-Seq experiments we have the opportunity to detect and
 measure antisense transcription, important since antisense transcripts
 impact gene transcription in several different ways. Stranded RNA-Seq
 determines the strand from which an RNA fragment originates, and so can
 be used to identify where antisense transcription may be implicated in
 gene regulation.
 .
 However, spurious antisense reads are often present in experiments, and
 can manifest at levels greater than 1% of sense transcript levels. This
 is enough to disrupt analyses by causing false antisense counts to
 dominate the set of genes with high antisense transcription levels.
 .
 The RoSA (Removal of Spurious Antisense) tool detects the presence of
 high levels of spurious antisense transcripts, by:
  * analysing ERCC spike-in data to find the ratio of antisense:sense
    transcripts in the spike-ins; or
  * using antisense and sense counts around splice sites to provide a
    set of gene-specific estimates; or
  * both.
 .
 Once RoSA has an estimate of the spurious antisense, expressed as a
 ratio of antisense:sense counts, RoSA will calculate a correction to
 the antisense counts based on the ratio. Where a gene-specific estimate
 is available for a gene, it will be used in preference to the global
 estimate obtained from either spike-ins or spliced reads.

Remark: This package is maintained by Steffen Moeller at
https://salsa.debian.org/med-team/rosa

Hi

(Dylan, please see below)

Would you mind explaining what you did for a build time test?  I've
added an autopkgtest for the R part.
used.  For instance the R packages do not seem to be needed:  dh-make-R
does not find any needed dependencies and the autopkgtest is passing.

@Dylan: Any idea how to fix

E: r-other-rosa: requires-r-api
N:
N:    This package ships a site library for the R programming language package
N:    but does not declare the R API r-api-<N> as a package prerequisite.
N:
N:    With the dh sequencer, please use --buildsystem=R in debian/rules and
N:    add the substitution variable ${R:Depends} to the Depends field in
N:    debian/control.
N:
N:    Refer to https://wiki.debian.org/Teams/r-pkg-team for details.
N:
N:    Severity: error
N:
N:    Check: languages/r/site-library
N:


Kind regards

      Andreas.

Hi Andreas,

Le sam. 4 juil. 2020 à 09:43, Andreas Tille <andreas@an3as.eu> a écrit :

\o/ this tag is finally useful :-)

I pushed a change that should fix this issue. I was not able to test
because r-cran-lsd is not available (still in NEW). Could you try this
change for me?

Best,
Dylan

Hi Dylan,

Sure it is!

While I think your changes are pretty sensible it does not solve the
problem.

Kind regards

     Andreas.

Le sam. 4 juil. 2020 à 11:27, Andreas Tille <tille@debian.org> a écrit :

:-( I will investigate this again later today


Dylan