arendsee / coding-group Goto Github PK

We can use the issues as a sort of chat room to talk about each problem.

I kind of went on a tangent with this project, doing a bit more than necessary. Don't think of my solutions as the solution. I don't really have a good solution to writing scientific analyses. There are lot possible approaches. I advocate R packages. But Jupiter notebooks are also popular. There are also approaches using workflow systems like snakemake or drake. Also there are graphical workflow systems like Galaxy (although I don't think they are generally powerful enough for bioinformaticians).

I hope in this repository we can explore a lot of possibilities. That said, and since we are all working on the Synder vignettes as well, I would like to spend a little time working on R packages. I might post this as problem 2. To make a simple R package that downloads a file, asserts that it is properly formatted, and loads it.

I'll keep on building on Problem 1. Retrieving, cleaning, and documenting a collection of data really is one of the hardest technical problems in bioinformatics. It can turn into a huge time sink and terrible source of bugs.

I've just opened Problem 2. This one is about building simple R packages. See problems/2/README for more info. If you have any questions, you can post them here.

Hi everyone,

I am currently not able to use Googleproducts or Slack, so my only line of communication is through github. If you want to talk to me, it is best to do so through these issues pages. Note that these are public.

This should only be a temporary problem, I'll sort out a VPN soon.

That said, github has a lot of awesome support for collaborative work. The issues page provides all the functionallity of a normal web forum. The projects page allows for task management, TODO lists, and the like. The wiki is, well, a wiki (a bunch of pages that anyone can edit). The project home page is static page which only authorized people can edit. We can explore all of these through this repo.