Last updated: 2024-12-30

Checks: 1 1

Knit directory: reproduce_genomics_paper_figures/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

The R Markdown is untracked by Git. 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: d2e0e8a

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 d2e0e8a. 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:    .DS_Store
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    data/fastq/
    Ignored:    data/public_data/
    Ignored:    data/reference/

Untracked files:
    Untracked:  analysis/04_figure1_a_b_c.Rmd
    Untracked:  analysis/05_figure1_d_f.Rmd
    Untracked:  analysis/06_figure1_g_h.Rmd
    Untracked:  analysis/07_figure1_i_j_k.Rmd
    Untracked:  analysis/08_homework.Rmd

Unstaged changes:
    Modified:   .gitignore
    Modified:   README.md
    Modified:   analysis/03_generate_bigwig.Rmd
    Modified:   analysis/index.Rmd
    Modified:   reproduce_genomics_paper_figures.Rproj

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.

There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.

Now that you have followed along to reproduce a figure from a paper, it is time for you to do it alone.

Go and read this paper Integrative epigenetic taxonomy of primary prostate cancer and try to reproduce Figure 2.

All ChIP-seq and RNA-seq data generated in this study are deposited in the Gene Expression Omnibus (GEO) database under the accession numbers GSE120738 and GSE120741.