Last updated: 2023-09-28

Checks: 2 0

Knit directory: cirrhosis-metabolism/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


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.

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 1eb8773. 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:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/other/
    Ignored:    data/.DS_Store
    Ignored:    data/README.html
    Ignored:    data/annotation/
    Ignored:    data/data.zip
    Ignored:    data/meta-mouse-vs-human/
    Ignored:    data/mouse-chronic-ccl4/
    Ignored:    data/output.zip
    Ignored:    figures/.DS_Store
    Ignored:    figures/ADH_ALDH.pdf
    Ignored:    figures/ADH_ALDH_hs.pdf
    Ignored:    figures/Blood.pdf
    Ignored:    figures/Blood_hs.pdf
    Ignored:    figures/CYP.pdf
    Ignored:    figures/CYP_hs.pdf
    Ignored:    figures/Canalicular.pdf
    Ignored:    figures/Canalicular_hs.pdf
    Ignored:    figures/DH.pdf
    Ignored:    figures/DH_hs.pdf
    Ignored:    figures/EPH.pdf
    Ignored:    figures/EPH_hs.pdf
    Ignored:    figures/FMO.pdf
    Ignored:    figures/FMO_hs.pdf
    Ignored:    figures/Figure 3.pptx
    Ignored:    figures/GST.pdf
    Ignored:    figures/GST_hs.pdf
    Ignored:    figures/MAO.pdf
    Ignored:    figures/MAO_hs.pdf
    Ignored:    figures/MT.pdf
    Ignored:    figures/MT_hs.pdf
    Ignored:    figures/NAT.pdf
    Ignored:    figures/NAT_hs.pdf
    Ignored:    figures/SULT.pdf
    Ignored:    figures/SULT_hs.pdf
    Ignored:    figures/UGT.pdf
    Ignored:    figures/UGT_hs.pdf
    Ignored:    figures/collages.pptx
    Ignored:    figures/correlation_1.pdf
    Ignored:    figures/correlation_2.pdf
    Ignored:    figures/correlation_3.pdf
    Ignored:    figures/heatmap.pdf
    Ignored:    figures/pca_plot.pdf
    Ignored:    output/.DS_Store
    Ignored:    output/mouse-chronic-ccl4/.DS_Store
    Ignored:    output/mouse-chronic-ccl4/carrier_genes.rds
    Ignored:    output/mouse-chronic-ccl4/correlations.rds
    Ignored:    output/mouse-chronic-ccl4/enrichment_result.rds
    Ignored:    output/mouse-chronic-ccl4/genesets_degs.rds
    Ignored:    output/mouse-chronic-ccl4/genesets_degs_hs.rds
    Ignored:    output/mouse-chronic-ccl4/metabolic_genes.rds
    Ignored:    output/mouse-chronic-ccl4/pca_result.rds
    Ignored:    output/mouse-chronic-ccl4/translated_hs_limma_result.rds
    Ignored:    output/seddik/
    Ignored:    renv/library/
    Ignored:    renv/sandbox/
    Ignored:    renv/staging/
    Ignored:    tables/metabolic_carrier_genes.xlsx

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
html 516a1f5 christianholland 2023-01-08 Build site.
Rmd 6013bfc christianholland 2023-01-08 wflow_publish("analysis/index.Rmd")
html d429adc christianholland 2023-01-08 Build site.
html 4323bde christianholland 2023-01-08 Build site.
Rmd 08bc4b3 christianholland 2023-01-08 wflow_publish("analysis/*.Rmd")
html d8910e2 christianholland 2023-01-07 Build site.
html b620f23 christianholland 2023-01-07 Build site.
html f6344b8 christianholland 2023-01-07 Build site.
Rmd eb21d53 christianholland 2023-01-07 wflow_publish("analysis/index.Rmd")
html 36c70d3 christianholland 2022-12-20 Build site.
html 5b439f5 christianholland 2022-12-08 Build site.
html 0258d2a christianholland 2022-12-07 Build site.
html 535b720 christianholland 2022-12-01 Build site.
html 72bb7f1 christianholland 2022-11-29 Build site.
html bacff3d christianholland 2022-11-29 Build site.
html e78a072 christianholland 2022-11-28 Build site.
html 2d6e308 christianholland 2022-11-28 Build site.
html 737882f christianholland 2022-10-27 Build site.
html d388f23 christianholland 2022-10-25 Build site.
Rmd 1793f24 christianholland 2022-10-24 Start workflowr project.

About

In this project the expression of genes involved in the metabolism of xenobiotic substances is analyzed in a mouse model that develops chronic liver disease induced by administration of CCl4 for 2, 6 and 12 months (Holland et al. 2021). In addition their expression in mouse is compared against the expression in patients that suffer from chronic liver disease utilizing a set of publicly available patient cohorts (see Table 1 in Holland et al. (2021) for more details)

The focus is on the following gene families:

References

Holland, Christian H., Ricardo O. Ramirez Flores, Maiju Myllys, Reham Hassan, Karolina Edlund, Ute Hofmann, Rosemarie Marchan, et al. 2021. “Transcriptomic Cross-Species Analysis of Chronic Liver Disease Reveals Consistent Regulation Between Humans and Mice.” Hepatology Communications 6 (1): 161–77. https://doi.org/10.1002/hep4.1797.