Downstream Analysis Feature Pack

Sydney-Informatics-Hub / Shotgun-Metagenomics-Analysis

Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more

GNU General Public License v3.0

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Downstream Analysis Feature Pack #2

Open hlydecker opened 2 years ago

hlydecker commented 2 years ago

We will be adding in a whole suite of features to support a wide variety of downstream data analysis using the outputs of our metagenomics pipeline.

Current planned features:

[ ] Exploring and visualising metagenomics data
[ ] Importing sample metadata and exploring trends based on a wide variety of metadata variables
[ ] Assessing statistical trends in differences between sample groups.

hlydecker commented 2 years ago

@calliza @tracychew @georgiesamaha @nandan75 what are your thoughts on how to best implement this? I am considering a folder containing one R markdown for data prep, another for analysis, and they both will create plot objects that will feed into a report R markdown.

Another option is that I could make a Docker container that builds an R environment, runs analysis and stuff, and then renders the outputs to a Shiny dashboard or a static R markdown html report.

georgiesamaha commented 9 months ago

Pretend this response was written on 12th April 2022.

Sounds like some great ideas, might be easiest to focus on the report and not a shiny dashboard at this stage. Lets chat