[Bioc-devel] Opinions on a meta-annotation package

Panagiotis Moulos mou|o@ @end|ng |rom ||em|ng@gr
Mon Oct 21 04:56:39 CEST 2019

Dear developers,

I maintain two packages (metaseqR, recoup) and about to submit an enhanced
(but different in many points, thus a new package) version of the 1st
(metaseqR2). During their course of development, maintenance and usage,
these packages have somehow come to use a common underlying annotation
system for the genomic regions they operate on, which of course makes use
of Bioconductor facilities and of course structures (GenomicRanges,
GenomicAlignments, BSgenome, GenomicFeatures etc.)

This annotation system:
- Builds a local SQLite database
- Supports certain "custom" genomic features which are required for the
modeling made by these packages
- Is currently embedded to each package
- Has almost evolved to a package of its own with respect to independent

The reason for this mail/question is that I would like to ask your opinion
whether it is worthy to create a new package to host  the annotation
functions and detach from the other two. Some points to support this idea:

1. It's used in the same manner by two other packages, thus there is a lot
of code  repetition
2. Users (including myself) often load one of these packages just to use it
to fetch genomic region annotations for other purposes outside the scope of
each package (metaseqR - RNA-Seq data analysis, recoup - NGS signal
3. It automatically constructs the required annotation regions to analyze
Lexogen Quant-Seq data (a protocol we are using a lot), a function which
may be useful to many others
4. The database created can be expanded with custom user annotations using
a GTF file to create it (making use of makeTxDbFromGFF)
5. Supports various annotation sources (Ensembl, UCSC, RefSeq, custom) in
one place
6. Has a versioning system, allowing transparency and reproducibility when

Some (maybe obvious) points against this idea:

1. Bioconductor has already a robust and rich genomic annotation system
which can be used and re-used as necessary
2. Maybe there is no need for yet another annotation-related package
3. There is possibly no wide acceptance for such a package, other than my
usage in the other two, and maybe a few more users that make use of the
annotation functionalities
4. Does not follow standard Bioconductor guidelines for creating annotation
packages (on the other hand it's not an annotation package in the strict
sense, but more a meta-annotation package).

Do you have any thoughts or opinions on the best way of action?

Best regards,


*Panagiotis Moulos, PhD*
*SNF researcher in Bioinformatics,*
*BSRC 'Alexander Fleming'*
*Fleming 34, 16672, Vari, Greece*
*Tel: +30 210 9656310, int. 131*
*Skype: panos_mou*

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