Last updated: 2019-03-07
workflowr checks: (Click a bullet for more information) ✔ 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: 934cda8
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: analysis/.DS_Store
Ignored: data/.DS_Store
Untracked files:
Untracked: analysis/README.md
Untracked: analysis/queen_pheromone.Rmd
Untracked: bioinformatics scripts/
Untracked: code/Script to make the donut plot.R
Untracked: code/Script to run multivariate brms model.R
Untracked: code/Script to set up for GO analyses.R
Untracked: code/pdf_supplementary_material.Rmd
Untracked: code/pdf_supplementary_material.pdf
Untracked: code/wojciechowski_histone_analysis.R
Untracked: data/apis.org.db
Untracked: data/apis_gene_comparisons/
Untracked: data/brms_model.txt
Untracked: data/brms_model_comparisons.rds
Untracked: data/brms_model_summary.rds
Untracked: data/component spreadsheets of queen_pheromone.db/
Untracked: data/gene_set_collection.RData
Untracked: data/gene_set_collection_kegg.RData
Untracked: data/morandin_comparison_data/
Untracked: data/most.pheromone.sensitive.genes.rds
Untracked: data/queen_pheromone.db
Untracked: docs/figure/
Untracked: figures/
Untracked: manuscript/
Untracked: supplement/
Unstaged changes:
Modified: .gitignore
Deleted: data/README.md
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.
File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | 934cda8 | Luke Holman | 2019-03-07 | First commit of new website structure |
Rmd | 6715b66 | Luke Holman | 2019-03-07 | Start workflowr project. |
This website presents all the code used for the paper Comparative transcriptomics of social insect queen pheromones by Holman, Helantera, Trontti, and Mikheyev (2019, Nature Communications).
Click here to see all the bash and Python scripts used to prepare the RNA-seq data and measure differential gene expression. Primary author: Sasha Mikheyev.
Click here to see a report generated with R Markdown, which details all statistical analyses, and generates all the figures and tables. Primary author: Luke Holman.
This reproducible R Markdown analysis was created with workflowr 1.1.1