Road to Bioc

[federicomarini]

Here's a list of items that likely will need to be addressed if we want annoFuse included in Bioconductor

• [x] expand the vignettes (e.g. nice ideas could come from the current doc folder)

• [x] roxygen to fully document the package and precisely specifying importFrom commands

• [x] examples to showcase the usage of functions

• [x] a NEWS.md file would not hurt?

• [x] specification of some biocViews to define the "landing area"

• [x] link to some potential output files to use as showcasing? (could be then plugged in e.g. into the shiny app)

• [x] version number to be adjusted (0.99.0 for submission

• [ ] related to the examples - it is a nice thing if we had unit tests, would make the code pretty robust to the nasty edge cases 😃

We could split them up to single issues for easier tracking, if desired! Federico

[federicomarini]

A first draft of the news can be found in https://github.com/federicomarini/annoFuse/commit/c5c0fe468d503100a57485692c495c7bbb234167

[kgaonkar6]

Will github links work for output formats work? Like https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/fusion_filtering/results/pbta-fusion-putative-oncogenic.tsv

[federicomarini]

biocViews suggestions are in https://github.com/federicomarini/annoFuse/commit/9595fffc588d6979ae3b4a60afa3ed79fb72e315, see if you think some might be still missing

[federicomarini]

Will github links work for output formats work

You mean when you enter them when calling the app? Gotta check that, not sure it will