[Bioc-devel] Question about external algorithms to Bioconductor package

Ioannis Vardaxis ioannis.vardaxis at ntnu.no
Sun Nov 12 23:11:57 CET 2017

I have developed a package and is current under review from
Bioconductor. In the future I am considering of making some changes to
the package, basically adding more functions etc.
My package is currently a peak calling algorithm where the input it gets
is either a BAM or SAM format. Because in general a user which runs such
analysis needs to, for example, map the DNA sequences to the reference
genome and obtaining the BAM/SAM file and then turn to my algorithm for
the rest. I was wondering if I am allowed to add those processes to my
package as preliminary stages such that it becomes easier for the user
to have everything in one place.
To do so I will need my package to make use of: SRAtoolkit, bowtie and
SAMtools. Which  I could run in terminal (using system() in R). For
running those stages need the user to have installed those algorithms
off course.
I was wondering if I am allowed to make use of those algorithms  in my
bioconductor package, with the appropriate references off course.
Ioannis Vardaxis
Stipendiat IMF

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