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workflowr

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Last updated: 2020-12-11

Checks: 2 0

Knit directory: R_gene_analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2.9000). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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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: 83dc49a

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 83dc49a. 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/

Untracked files:
    Untracked:  data/Brec_R1.txt
    Untracked:  data/Brec_R2.txt
    Untracked:  data/CR15_R1.txt
    Untracked:  data/CR15_R2.txt
    Untracked:  data/CR_14_R1.txt
    Untracked:  data/CR_14_R2.txt
    Untracked:  data/KS_R1.txt
    Untracked:  data/KS_R2.txt
    Untracked:  data/NBS_PAV.txt.gz
    Untracked:  data/NLR_PAV_GD.txt
    Untracked:  data/NLR_PAV_GM.txt
    Untracked:  data/PAVs_newick.txt
    Untracked:  data/PPR1.txt
    Untracked:  data/PPR2.txt
    Untracked:  data/SNPs_newick.txt
    Untracked:  data/bac.txt
    Untracked:  data/brown.txt
    Untracked:  data/cy3.txt
    Untracked:  data/cy5.txt
    Untracked:  data/early.txt
    Untracked:  data/flowerings.txt
    Untracked:  data/foregeye.txt
    Untracked:  data/height.txt
    Untracked:  data/late.txt
    Untracked:  data/mature.txt
    Untracked:  data/motting.txt
    Untracked:  data/mvp.kin.bin
    Untracked:  data/mvp.kin.desc
    Untracked:  data/oil.txt
    Untracked:  data/pdh.txt
    Untracked:  data/protein.txt
    Untracked:  data/rust_tan.txt
    Untracked:  data/salt.txt
    Untracked:  data/seedq.txt
    Untracked:  data/seedweight.txt
    Untracked:  data/stem_termination.txt
    Untracked:  data/sudden.txt
    Untracked:  data/virus.txt
    Untracked:  data/yield.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.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/about.Rmd) and HTML (docs/about.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
html	83dc49a	Philipp Bayer	2020-12-11	Trace deleted files
html	dae157b	Philipp Bayer	2020-09-24	Update of analysis
Rmd	1b346e9	Philipp Bayer	2020-09-22	More data!
html	1b346e9	Philipp Bayer	2020-09-22	More data!
html	0777e1d	Philipp Bayer	2020-09-22	update
html	e6e9b9b	Philipp Bayer	2020-09-21	Build site.
Rmd	c71005a	Philipp Bayer	2020-09-18	lots changes
html	c71005a	Philipp Bayer	2020-09-18	lots changes
html	efd6af1	Philipp Bayer	2020-09-18	wflow_git_commit(all = T)
Rmd	8a6560a	Philipp Bayer	2020-09-17	Start workflowr project.

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In this project I dig deeper into NLR/RLK/RLP genes of the recent soybean pangenome.