Last updated: 2018-08-25

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• ✔ 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: a865fa3

  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:    .Rhistory
      Ignored:    .Rproj.user/
      Ignored:    .vscode/
      Ignored:    code/.DS_Store
      Ignored:    data/raw/
      Ignored:    src/.DS_Store
      Ignored:    src/.ipynb_checkpoints/
      Ignored:    src/Rmd/.Rhistory
  
  Untracked files:
      Untracked:  Snakefile_clonality
      Untracked:  Snakefile_somatic_calling
      Untracked:  code/analysis_for_garx.Rmd
      Untracked:  code/selection/
      Untracked:  code/yuanhua/
      Untracked:  data/canopy/
      Untracked:  data/cell_assignment/
      Untracked:  data/de_analysis_FTv62/
      Untracked:  data/donor_info_070818.txt
      Untracked:  data/donor_info_core.csv
      Untracked:  data/donor_neutrality.tsv
      Untracked:  data/exome-point-mutations/
      Untracked:  data/fdr10.annot.txt.gz
      Untracked:  data/human_H_v5p2.rdata
      Untracked:  data/human_c2_v5p2.rdata
      Untracked:  data/human_c6_v5p2.rdata
      Untracked:  data/neg-bin-rsquared-petr.csv
      Untracked:  data/neutralitytestr-petr.tsv
      Untracked:  data/sce_merged_donors_cardelino_donorid_all_qc_filt.rds
      Untracked:  data/sce_merged_donors_cardelino_donorid_all_with_qc_labels.rds
      Untracked:  data/sce_merged_donors_cardelino_donorid_unstim_qc_filt.rds
      Untracked:  data/sces/
      Untracked:  data/selection/
      Untracked:  data/simulations/
      Untracked:  data/variance_components/
      Untracked:  docs/figure/selection_models.Rmd/
      Untracked:  figures/
      Untracked:  output/differential_expression/
      Untracked:  output/donor_specific/
      Untracked:  output/line_info.tsv
      Untracked:  output/nvars_by_category_by_donor.tsv
      Untracked:  output/nvars_by_category_by_line.tsv
      Untracked:  output/variance_components/
      Untracked:  references/
      Untracked:  tree.txt
  
  

  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
html	090c1b9	davismcc	2018-08-24	Build site.
html	d2e8b31	davismcc	2018-08-19	Build site.
html	1489d32	davismcc	2018-08-17	Add html files
Rmd	6b5f8c7	davismcc	2018-08-17	Updating organisational pages.
html	9856275	davismcc	2018-08-07	Build site.
Rmd	5fc189d	davismcc	2018-08-07	Start workflowr project.

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This reproducible R Markdown analysis was created with workflowr 1.1.1

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