Topic brainstorm

[BrunoGrandePhD]

Comment below with topics that you would like to see included in this set of intermediate/advanced R tutorials for genomic data analysis. You don't need to know the topic, because someone else might be able to write the tutorial. Also, a topic can be anything in R that can be used for genomic data analysis, e.g. an R package.

We'll then create separate GitHub issues for each topic that will get assigned to someone.

[BrunoGrandePhD]

Here are a few R packages that I think deserve a genomic-focused tutorial.

• Shiny for interactive visualization in genomics
• data.table for efficiently manipulating large datasets
• ggplot2 for visualizing genomic data
• R Markdown for generating self-contained reports

[zhenyisong]

These are tools used in our project. But I am not sure what is biological story? RNA (mRNA or lncRNA)? ChIP-seq (Broad or narrow?) ? Whole Genome Analysis? Or cover all these issues?

[privefl]

Does there exist a dataset with all these data (for example, trying to combine all these information)?

[BrunoGrandePhD]

Feel free to continue posting ideas of topics that should be converted into genomics-focused tutorials.

Once you're interested in developing a tutorial on one of the suggested ideas (or one of your own), create a new issue here. I'll be posting contribution guidelines shortly.

[BrunoGrandePhD]

Check out the contributing guidelines here:
https://github.com/hackseq/2017_project_5/blob/master/contributing.md

[BrunoGrandePhD]

Here are some additional ideas:

• purrr for functional programming
• sva for batch effect correction (despite being on Bioconductor, the vignette isn't that good)
• Any number of unsupervised or supervised machine learning or clustering packages
• Gene set enrichment analysis (despite there being multiple package for this, I always have a hard time to find a simple tutorial on how to do this)
• feather for fast data frame reading and writing

[zhenyisong]

@BrunoGrande if sva and/or supervised learning, then choosing the dataset is picky. GSEA, I prefer using clusterProfiler.