Last updated: 2026-01-13

Checks: 2 0

Knit directory: Dissrt/

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: 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: b31faa7

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 b31faa7. 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/
    Ignored:    data/cmf/
    Ignored:    data/counts/
    Ignored:    data/de/
    Ignored:    data/genesets/
    Ignored:    data/theme/

Unstaged changes:
    Deleted:    DDR_DEGs_direction.RDS
    Deleted:    DOX_vs_NUTL_logFC_correlation.pdf_251003.pdf
    Deleted:    DOX_vs_NUTL_logFC_correlation.pdf_251003.png
    Deleted:    PCA_2hr_HC_filt2_PC1_PC2_EMP_251010.png, folder = output_folder, height = 5, width = 5_251010.pdf
    Deleted:    PCA_2hr_HC_filt2_PC1_PC2_EMP_251010.png, folder = output_folder, height = 5, width = 5_251010.png
    Deleted:    PCA_2hr_HC_filt2_PC1_PC2_EMP_251010.png, folder = output_folder, height =5, width = 5_251010.pdf
    Deleted:    PCA_2hr_HC_filt2_PC1_PC2_EMP_251010.png, folder = output_folder, height =5, width = 5_251010.png
    Deleted:    Volcano_24hr_Legend_EMP.png
    Modified:   analysis/CMF.Rmd
    Modified:   analysis/RNASeq_QC.Rmd

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 repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.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
Rmd b31faa7 Emma M. Pfortmiller 2026-01-13 Initialize Analysis Website 01/13/26
html be6bf98 Emma M. Pfortmiller 2025-09-26 Build site.
Rmd a881ac1 Emma M. Pfortmiller 2025-09-26 Start workflowr project.

Welcome!

This website is a working archive for the analysis I’m completing for this project. Click below to look at each piece of my analysis within our workflow.