Last updated: 2019-02-14

workflowr checks: (Click a bullet for more information)

• ✖ R Markdown file: uncommitted changes

  The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

• ✔ Repository version: fcaa341

  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/
      Ignored:    analysis/Quality_metrics_cache/
  
  Untracked files:
      Untracked:  analysis/enrichment.Rmd
      Untracked:  analysis/figure/
      Untracked:  data/SNP_200000.txt
      Untracked:  data/SNP_50000.txt
      Untracked:  data/SNP_500000.txt
      Untracked:  data/edgeR-lrt-10%filter_res.Rd
      Untracked:  data/edgeR-qlf-10%filter_res.Rd
  
  Unstaged changes:
      Modified:   .gitignore
      Modified:   analysis/DEseq2-LRT.Rmd
      Modified:   analysis/EdgeR-LRT.Rmd
      Modified:   analysis/EdgeR-QLF.Rmd
      Modified:   analysis/Quality_metrics.Rmd
      Modified:   analysis/index.Rmd
      Modified:   code/summary_functions.R
      Modified:   cropseq.Rproj
      Modified:   data/DE_input.Rd
  
  

  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	fcaa341	simingz	2018-12-17	explore filtering
html	fcaa341	simingz	2018-12-17	explore filtering
Rmd	49ecf6e	simingz	2018-12-16	explore filtering
html	49ecf6e	simingz	2018-12-16	explore filtering
html	6b6ebde	simingz	2018-12-14	fix Xin’s comment for qc
html	21193c8	simingz	2018-12-10	website
Rmd	7c8478e	simingz	2018-12-10	website
html	b94b65a	simingz	2018-12-05	de_anlysis
Rmd	8ce79ed	simingz	2018-12-05	de_anlysis
html	275d5d8	simingz	2018-12-02	qc
html	9f8ba8d	szhao06	2018-12-02	qc
html	c206c9d	szhao06	2018-12-01	qc
Rmd	fdd5647	szhao06	2018-12-01	qc
html	fdd5647	szhao06	2018-12-01	qc
html	6360503	simingz	2018-11-20	Build site.
Rmd	8be64d0	simingz	2018-11-20	First
Rmd	fe55f5d	simingz	2018-11-19	Start workflowr project.

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This reproducible R Markdown analysis was created with workflowr 1.1.1

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