Improve the documentation for `tidybulk`

[stemangiola]

• improving examples for methods
• solving documentation warnings (when packages are loading or installing)
• Improving methods' argument description
• improving the transparency of the method used in the backend in the description of the methods

[aliosmancetin]

Hi, I'd like to contribute this one, but I am not sure how it should be done or when is the deadline. I am a medical doctor but currently a PhD student as a computational biologist of my group. I know transcriptomics analysis with bioconductor and I like tidy paradigm. Since this is labeled as a "good first issue", if there will be enough guidance, I can give it a try, what do you think?

[stemangiola]

Thanks @aliosmancetin! Nice to meet you.

I am not sure when is the deadline

There is a soft deadline to commit and start working, so we can form the team for the upcoming paper. But there is no hard deadline for completing the task. We trust the community on that side. Of course, each challenge should not drag too long, so to keep the ball rolling.

I am not sure how it should be done

• Assign yourself to this issue,
• Read about Roxigen2 https://cran.r-project.org/web/packages/roxygen2/vignettes/roxygen2.html
• Fork tidybulk
• Look at all available methods in the R/methods.R script
• For each of those methods, look at the documentation (e.g. ?test_differential_abundance)
• For each argument in each method, judge if it is very, very easily understandable; if the answer is not (as I expect for the majority of them), try to improve it.
• Is the output structure and class clearly described in the documentation? If not, you can improve that.
• Are examples covering most argument combinations and use cases, if not you can add more examples

Then, other more challenging tasks are

• solving documentation warnings (when packages are loading or installing)
• Make sure that the backend code for each method is pasted and described in the @description part of the documentation to give transparency of what is happening underneath.
• For all analysis methods, create messaging framework, to communicate to the user the operations that are running below (e.g, "tidybulk says: normalising with TMM", "tidybulk says: estimating .. with xxx")

Let me know if you want more guidance. @HelenaLC might be a good code reviewer, as she is an expert on R packages and standards.

[aliosmancetin]

Nice to meet you too! Thanks for your comments and outline. It seems doable for me, I'll start asap.

[aliosmancetin]

I couldn't figure out how to assign myself. Should ".take" work or not?

[stemangiola]

I assigned you. Not sure if users can choose their name from the drop-down menu

Looking forward to you PR!

[stemangiola]

Hello @aliosmancetin , just to do some planning on our side.

Do you have a timeline already to work on this challenge?

A note: for the tidy adapters, please follow the tidySingleCellExperiment package, which was very recently revamped.

[aliosmancetin]

Hi @stemangiola,

If you refer very structured work-plan with "timeline", no, I don't have unfortunately 😅 But, I've already started to read must-read documents. I am willing to commit some work on this issue, but I am not sure how long it takes.

[stemangiola]

Hi @stemangiola,

If you refer very structured work-plan with "timeline", no, I don't have unfortunately 😅 But, I've already started to read must-read documents. I am willing to commit some work on this issue, but I am not sure how long it takes.

I assigned you prematurely. Now I have emptied the assignee field, so you can assign yourself when you will be ready, with no rush :)

[aliosmancetin]

I assigned you prematurely. Now I have emptied the assignee field, so you can assign yourself when you will be ready, with no rush :)

Okay, let me focus on this one more week. Then we can discuss my progress and whether it's going to work or not.