I have recently completed novel bioconductor package aims to analyze ChIP-Seq data, and I want to make a publication on this work. BTW, this is my very first publication in my grad studies and choosing Bioinformatics journal could be the best way but it is challenging because this journal has a relatively high impact factor. The point is, my package has been submitted to Bioconductor a month ago but still under evaluation. I already make revision based on the request from Bioconductor team, but they still haven't finished the package review yet. My main concern is, package implementation is done fairly efficient (after revision, now it is really fast) but not very much functionality (5 o 6 functions for ChIP-seq workflow, mainly investigating ChIP-Seq peaks). Due to my experience in bioinformatics and R are limited, so the implementation of my packages hasn't reached advanced desired level for publication of Bioinformatics journal. Bioconductor mentioned that I have to improve the code quality as well.
From my point of view, submitting my packages to Bioinformatics could be risky, so I am looking for the alternative avenue to make medium level research publication in Bioinformatics. I believe there is must be a way to make this sort of publication work for grad students in CS. My package is fairly well done but can't be immediately accepted by Bioconductor project in this times, so I want to make publication in another way. Can anyone direct me which avenue I could give it try? How can I make ease publication in bioinformatics? Can anyone instruct me which journal or publication group I could give my paper? Any further assistance? Thanks in advance :)
@Jean: Dear Jean, thanks for your respond. The point is, my packages aims to analyze ChIP-Seq data, so choosing bioconductor for package submission is my first attempt, but it still takes a lot of time to improve it. Another point is, my package depends on few important bioconductor infrastructure package to make ease the genomic data analysis, so I afraid my package won't suit for CRAN. Could you make your answer bit more clear? Thank you :)
I was only suggesting releasing your software on CRAN as the requirements there seem lighter than for Bioconductor. If your package is ready for public consumption, I think you should make it available without waiting for a publication. This would allow you to collect feedback from users so that you may still improve it before publication.
@Jean: Yes, I already did create my projects on GitHub, it is available to the public. Don't know how to attract the potential user to let them try out and collect feedback. Bioconductor said my package is interesting but it hasn't reached Bioconductor standards (I mean, they need very well-done code to be accepted, my package is already efficient unless few drawback). Any effective strategy to ask experienced people to let the package try and getting their opinion? I am sorry for my naive question. Thank you:)
Posting on Biostars is a good start, try also other places visited by your target audiences (e.g. maybe SEQanswers). Maybe create a post in the the Tools section here. As has been discussed elsewhere, people will use a software either because it is the most convenient or it provides functionality not available elsewhere. If your package is doing the same things as others, you may have a hard time convincing users to switch from what they already use.