AlexsLemonade / AlexsLemonade/refinebio-examples

Microarray Analysis Updates: Pathway Analysis - QuSage notebooks

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Description

We need the main update items listed on #173 to happen here :

> - Have the getting started template material added to it (# 146)
> - Update to adhere to the style guide (#148)
> - Add the dataset added to the S3 bucket. (See https://github.com/AlexsLemonade/refinebio-examples/blob/master/CONTRIBUTING.md#adding-datasets-to-the-s3-bucket)
> - Add to the Snakefile and render with snakemake on the Docker container.

There's a set of QuSage notebooks for microarray that all need to revamped. They should be evaluated as a set.

Contributor guide

Open the contributing guide

Research direction

Start by reading the updates in #173, the getting-started material in #146, the style guide work in #148, and the CONTRIBUTING.md instructions for adding datasets to the S3 bucket. Review the QuSage microarray notebooks as a set, then check the Snakefile and render them in the Docker container. Done means the requested template, style, dataset, workflow entry, and rendered notebooks are all updated.

Written by the indexing model from the issue text.

Assessment

Tech stack
aws, docker, jupyter-notebook
Domain
bioinformatics, build-system, documentation
Issue type
Refactor
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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