Last updated: 2018-11-15

workflowr checks: (Click a bullet for more information)

• ✔ R Markdown file: up-to-date

  Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

• ✔ Repository version: 0cc76ea

  Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.
  
  Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

  
  Ignored files:
      Ignored:    .DS_Store
      Ignored:    .Rproj.user/
      Ignored:    .sos/
      Ignored:    analysis/.DS_Store
  
  Untracked files:
      Untracked:  .Rhistory
      Untracked:  dsc/
      Untracked:  notes/
  
  Unstaged changes:
      Modified:   .gitignore
      Modified:   analysis/_site.yml
      Deleted:    benchmark.dsc
      Deleted:    code/README.md
      Deleted:    code/config.yaml
      Deleted:    data/README.md
      Deleted:    data/metadata.rds
      Deleted:    data/rawcounts.rds
      Deleted:    modules/get_data.R
      Deleted:    modules/get_data.dsc
      Deleted:    modules/glm.dsc
      Deleted:    modules/run_DESeq2.R
      Deleted:    modules/run_DESeq2.dsc
      Deleted:    modules/t_test.dsc
      Deleted:    modules/wilcox_test.dsc
      Deleted:    output/README.md
  
  

  Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	0cc76ea	jhsiao999	2018-11-15	first commit
Rmd	2dd4a18	jhsiao999	2018-11-15	Start workflowr project.

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The DSC code is available under the MIT license. The text, simulated data and figures are available under the CC-BY license.

Both of these allow you to reuse, adapt, or redistribute the content as long as you attribute us. If you use our data, please attribute us as follows:

The simulated data was generated by the Stephens lab at the University of Chicago (see https://github.com/stephenslab/dsc-log-fold-change for details).

If you use our code, please attribute us as follows:

The code used to process the data was adapted from the code written by the Stephens lab lab at the University of Chicago (see https://github.com/stephenslab/dsc-log-fold-change for details).

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This reproducible R Markdown analysis was created with workflowr 1.1.1

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