Thanks Ge for the answer, and for all your work on CNEr. Me and some of my coworkers are still using your package, or at least a subset of its functions, typically after aligning genomes externally with the nf-core/pairgenomealign pipeline, which can output Axt format (CNEr input).
https://nf-co.re/pairgenomealign Actually, I also wrote an informal package that can load MAF or GFF from the same pipeline, and it would be straightforward to write a function that reads these files into CNEr::Axt objects. https://oist.github.io/GenomicBreaks/ Based on this, if nobody volunteers to maintain CNEr to its full extent, I would be happy to help to maintain a streamlined version that does not rely on compiled C code (a frequent source of bitrot) and does not support running external aligners (since there are now pipelines that can do it easily). Have a nice day, Charles _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel