Schedule:

8:45 - 9:00 Breakfast

9:00 - 10:30 Statistical inference I

10:30 - 10:50 Coffee break

10:50 - 12:00 Statistical inference II and plotting

12:00 - 1:30 Lunch

1:30 - 3:00 Reproducible reporting I - R Markdown and Batch effects

3:00 - 3:30 Coffee break

3:30 - 5:00 Reproducible reporting II - workflowr

Software installation:

Materials:

  1. Proper statistical inference: correct use of p-values and correlation (slides)

  2. Plots to avoid (slides)

  3. Tools for generating reproducible reporting: R markdown and workflowr (slides)

  4. Practice: a case study on batch effects

Resources:

  1. R Markdown by R studio

  2. workflowr webpage, (a simple example) and ([a more complicated example]https://jdblischak.github.io/singleCellSeq/analysis/)

  3. DataCamp course website
  4. eBook: Biomedical Data Science by Rafael Irizarry and Michael Love

Some reference papers:

  1. p-value and irreproducibility: Halsey, et al. (2015)
  2. Assessing reproducibility: Li, et al. (2011)
  3. A case study on batch effects: