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.

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:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/contrainedclustering.Rmd
    Untracked:  analysis/count.Rmd
    Untracked:  analysis/deconvSimulation2.Rmd
    Untracked:  analysis/ideas.Rmd
    Untracked:  analysis/methylation.Rmd
    Untracked:  code/sccytokines.R
    Untracked:  code/scdeCalibration.R
    Untracked:  data/bart/
    Untracked:  data/cytokine/DE_controls_output_filter10.RData
    Untracked:  data/cytokine/DE_controls_output_filter10_addlimma.RData
    Untracked:  data/cytokine/README
    Untracked:  data/cytokine/test.RData
    Untracked:  data/cytokine_normalized.RData
    Untracked:  data/deconv/
    Untracked:  data/scde/

Unstaged changes:
    Modified:   analysis/deconvSimulation.Rmd
    Modified:   analysis/deconvolution.Rmd
    Deleted:    data/mout_high.RData
    Deleted:    data/scCDT.RData
    Deleted:    data/sva_sva_high.RData

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