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 job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

The command set.seed(20240216) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

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Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 67d23a6. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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/
    Ignored:    code/voomByGroup/
    Ignored:    data/.DS_Store
    Ignored:    data/C133_Neeland/
    Ignored:    data/C133_Neeland_batch0/
    Ignored:    data/C133_Neeland_batch1/
    Ignored:    data/C133_Neeland_batch2/
    Ignored:    data/C133_Neeland_batch3/
    Ignored:    data/C133_Neeland_batch4/
    Ignored:    data/C133_Neeland_batch5/
    Ignored:    data/C133_Neeland_batch6/
    Ignored:    data/C133_Neeland_merged/
    Ignored:    renv/library/
    Ignored:    renv/staging/

Untracked files:
    Untracked:  analysis/13.1_DGE_analysis_macro-alveolar_cells_decontx.Rmd
    Untracked:  code/cellbender.sh
    Untracked:  code/move_files.R
    Untracked:  data/heart10k_raw_feature_bc_matrix.h5
    Untracked:  data/oshlack_lab/
    Untracked:  data/output.log
    Untracked:  data/tiny_output.log
    Untracked:  data/tiny_raw_feature_bc_matrix.h5ad

Unstaged changes:
    Modified:   .DS_Store
    Modified:   analysis/06.1_azimuth_annotation_decontx.Rmd
    Modified:   code/run_cellbender.R

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.