Last updated: 2019-03-07

Checks: 2 0

Knit directory: queen-pheromone-RNAseq/

This reproducible R Markdown analysis was created with workflowr (version 1.2.0). The Report tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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: 7d083c0

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:    analysis/.DS_Store
    Ignored:    bioinformatics_scripts/data/
    Ignored:    bioinformatics_scripts/ref/
    Ignored:    data/.DS_Store
    Ignored:    data/apis_gene_comparisons/.DS_Store
    Ignored:    data/apis_gene_comparisons/wojciechowski_histone_data/.DS_Store
    Ignored:    data/apis_gene_comparisons/wojciechowski_histone_data/GSE110640_RAW/.DS_Store
    Ignored:    data/apis_gene_comparisons/wojciechowski_histone_data/GSE110641_RAW/.DS_Store
    Ignored:    data/component spreadsheets of queen_pheromone.db/.DS_Store
    Ignored:    docs/figure/pdf_supplementary_material.Rmd/
    Ignored:    figures/
    Ignored:    manuscript/
    Ignored:    supplement/

Unstaged changes:
    Deleted:    bioinformatics_scripts/data
    Deleted:    bioinformatics_scripts/ref

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.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
html 7d083c0 lukeholman 2019-03-07 new theme
html f260a62 Luke Holman 2019-03-07 Build site.
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).

Bioinformatics

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.

Statistics and plotting

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.