Home
Last updated: 2021-03-29
Checks: 7 0
Knit directory: liver-disease-atlas/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). 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 job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20201218) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
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 91a5ed5. 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/01-mouse-chronic-ccl4_cache/
Ignored: analysis/02-mouse-acute-apap_cache/
Ignored: analysis/03-mouse-acute-ccl4_cache/
Ignored: analysis/04-mouse-acute-ph_cache/
Ignored: analysis/05-mouse-acute-bdl_cache/
Ignored: analysis/06-mouse-acute-lps_cache/
Ignored: analysis/07-mouse-acute-tunicamycin_cache/
Ignored: analysis/08-human-diehl-nafld_cache/
Ignored: analysis/09-human-hampe13-nash_cache/
Ignored: analysis/10-human-hampe14-misc_cache/
Ignored: analysis/11-human-hoang-nafld_cache/
Ignored: analysis/12-human-ramnath-fibrosis_cache/
Ignored: analysis/13-meta-chronic-vs-acute_cache/
Ignored: analysis/14-meta-mouse-vs-human_cache/
Ignored: analysis/15-plot-chronic-ccl4_cache/
Ignored: analysis/16-plot-acute-apap_cache/
Ignored: analysis/17-plot-acute-ccl4_cache/
Ignored: analysis/18-plot-acute-ph_cache/
Ignored: analysis/19-plot-acute-bdl_cache/
Ignored: analysis/20-plot-study-overview_cache/
Ignored: analysis/21-plot-chronic-vs-acute_cache/
Ignored: analysis/22-plot-mouse-vs-human_cache/
Ignored: analysis/23-plot-precision-recall_cache/
Ignored: analysis/24-save-tables_cache/
Ignored: code/.DS_Store
Ignored: code/README.html
Ignored: code/meta-mouse-vs-human/.DS_Store
Ignored: data.zip
Ignored: data/.DS_Store
Ignored: data/Icon
Ignored: data/annotation/
Ignored: data/human-diehl-nafld/
Ignored: data/human-hampe13-nash/
Ignored: data/human-hampe14-misc/
Ignored: data/human-hoang-nafld/
Ignored: data/human-ramnath-fibrosis/
Ignored: data/meta-chronic-vs-acute/
Ignored: data/meta-mouse-vs-human/
Ignored: data/mouse-acute-apap/
Ignored: data/mouse-acute-bdl/
Ignored: data/mouse-acute-ccl4/
Ignored: data/mouse-acute-lps/
Ignored: data/mouse-acute-ph/
Ignored: data/mouse-acute-tunicamycin/
Ignored: data/mouse-chronic-ccl4/
Ignored: external_software/.DS_Store
Ignored: external_software/README.html
Ignored: external_software/stem/.DS_Store
Ignored: figures/.DS_Store
Ignored: figures/Figure 1 (partial).pdf
Ignored: figures/Figure 1.pdf
Ignored: figures/Figure 1.png
Ignored: figures/Figure 2 (partial).pdf
Ignored: figures/Figure 2.pdf
Ignored: figures/Figure 2.png
Ignored: figures/Figure 3.pdf
Ignored: figures/Figure 3.png
Ignored: figures/Figure 4.pdf
Ignored: figures/Figure 4.png
Ignored: figures/Figure 5.pdf
Ignored: figures/Figure 6.png
Ignored: figures/Icon
Ignored: figures/Supplementary Figure 0.1.pdf
Ignored: figures/Supplementary Figure 0.1.png
Ignored: figures/Supplementary Figure 1.1.pdf
Ignored: figures/Supplementary Figure 1.1.png
Ignored: figures/Supplementary Figure 2.1.pdf
Ignored: figures/Supplementary Figure 2.1.png
Ignored: figures/Supplementary Figure 2.2.pdf
Ignored: figures/Supplementary Figure 2.2.png
Ignored: figures/Supplementary Figure 2.3.pdf
Ignored: figures/Supplementary Figure 2.3.png
Ignored: figures/Supplementary Figure 2.4.pdf
Ignored: figures/Supplementary Figure 2.4.png
Ignored: figures/Supplementary Figure 2.5.pdf
Ignored: figures/Supplementary Figure 2.5.png
Ignored: figures/Supplementary Figure 2.6.pdf
Ignored: figures/Supplementary Figure 2.6.png
Ignored: figures/Supplementary Figure 2.7.pdf
Ignored: figures/Supplementary Figure 2.7.png
Ignored: figures/Supplementary Figure 3.1.pdf
Ignored: figures/Supplementary Figure 3.1.png
Ignored: figures/Supplementary Figure 3.2.pdf
Ignored: figures/Supplementary Figure 3.2.png
Ignored: figures/Supplementary Figure 3.3.pdf
Ignored: figures/Supplementary Figure 3.3.png
Ignored: figures/Supplementary Figure 3.4.pdf
Ignored: figures/Supplementary Figure 3.4.png
Ignored: figures/Supplementary Figure 4.1.pdf
Ignored: figures/Supplementary Figure 4.1.png
Ignored: figures/Supplementary Figure 4.2.pdf
Ignored: figures/Supplementary Figure 4.2.png
Ignored: figures/Supplementary Figure 5.1.pdf
Ignored: figures/Supplementary Figure 5.1.png
Ignored: figures/figures.key
Ignored: figures/histologies.key
Ignored: figures/panels/
Ignored: figures/tmp/.DS_Store
Ignored: figures/tmp/Fig5A1.pdf
Ignored: figures/tmp/Fig5A2.pdf
Ignored: figures/tmp/Icon
Ignored: geo_submission/
Ignored: output/.DS_Store
Ignored: output/Icon
Ignored: output/README.html
Ignored: output/human-diehl-nafld/Icon
Ignored: output/human-diehl-nafld/limma_result.rds
Ignored: output/human-diehl-nafld/meta_data.rds
Ignored: output/human-diehl-nafld/normalized_expression.rds
Ignored: output/human-diehl-nafld/pca_result.rds
Ignored: output/human-diehl-nafld/z_scores.rds
Ignored: output/human-hampe13-nash/Icon
Ignored: output/human-hampe13-nash/limma_result.rds
Ignored: output/human-hampe13-nash/meta_data.rds
Ignored: output/human-hampe13-nash/normalized_expression.rds
Ignored: output/human-hampe13-nash/pca_result.rds
Ignored: output/human-hampe13-nash/z_scores.rds
Ignored: output/human-hampe14-misc/Icon
Ignored: output/human-hampe14-misc/limma_result.rds
Ignored: output/human-hampe14-misc/meta_data.rds
Ignored: output/human-hampe14-misc/normalized_expression.rds
Ignored: output/human-hampe14-misc/pca_result.rds
Ignored: output/human-hampe14-misc/z_scores.rds
Ignored: output/human-hoang-nafld/Icon
Ignored: output/human-hoang-nafld/limma_result.rds
Ignored: output/human-hoang-nafld/normalized_expression.rds
Ignored: output/human-hoang-nafld/pca_result.rds
Ignored: output/human-hoang-nafld/z_scores.rds
Ignored: output/human-ramnath-fibrosis/Icon
Ignored: output/human-ramnath-fibrosis/limma_result.rds
Ignored: output/human-ramnath-fibrosis/normalized_expression.rds
Ignored: output/human-ramnath-fibrosis/pca_result.rds
Ignored: output/human-ramnath-fibrosis/z_scores.rds
Ignored: output/meta-chronic-vs-acute/Icon
Ignored: output/meta-chronic-vs-acute/acute_gene_pool.rds
Ignored: output/meta-chronic-vs-acute/chronic_gene_pool.rds
Ignored: output/meta-chronic-vs-acute/exclusive_genes_characterization.rds
Ignored: output/meta-chronic-vs-acute/gene_membership.rds
Ignored: output/meta-chronic-vs-acute/gene_set_similarity.rds
Ignored: output/meta-chronic-vs-acute/go_cluster_ranking.rds
Ignored: output/meta-chronic-vs-acute/go_wordcounts.rds
Ignored: output/meta-chronic-vs-acute/interstudy_enrichment.rds
Ignored: output/meta-chronic-vs-acute/limma_result.rds
Ignored: output/meta-chronic-vs-acute/meta_data.rds
Ignored: output/meta-chronic-vs-acute/pca_dist.rds
Ignored: output/meta-chronic-vs-acute/ranked_common_genes.rds
Ignored: output/meta-chronic-vs-acute/ranked_exclusive_acute_genes.rds
Ignored: output/meta-chronic-vs-acute/ranked_exclusive_chronic_genes.rds
Ignored: output/meta-chronic-vs-acute/union_acute_geneset.rds
Ignored: output/meta-chronic-vs-acute/union_chronic_geneset.rds
Ignored: output/meta-mouse-vs-human/Icon
Ignored: output/meta-mouse-vs-human/chronic_mouse_deg_numbers.rds
Ignored: output/meta-mouse-vs-human/consistent_genes.rds
Ignored: output/meta-mouse-vs-human/cross_species_enrichment.rds
Ignored: output/meta-mouse-vs-human/cross_species_similarity.rds
Ignored: output/meta-mouse-vs-human/etiology_gene_sets.rds
Ignored: output/meta-mouse-vs-human/gene_set_similarity.rds
Ignored: output/meta-mouse-vs-human/go_cluster_ranking.rds
Ignored: output/meta-mouse-vs-human/go_wordcounts.rds
Ignored: output/meta-mouse-vs-human/gsea_res.rds
Ignored: output/meta-mouse-vs-human/individual_le.rds
Ignored: output/meta-mouse-vs-human/interstudy_enrichment.rds
Ignored: output/meta-mouse-vs-human/leading_edges.rds
Ignored: output/meta-mouse-vs-human/leading_edges_characterization.rds
Ignored: output/meta-mouse-vs-human/leading_edges_mgi.rds
Ignored: output/meta-mouse-vs-human/limma_result.rds
Ignored: output/meta-mouse-vs-human/meta_data.rds
Ignored: output/meta-mouse-vs-human/precision_recall.rds
Ignored: output/meta-mouse-vs-human/precision_recall_chronicity.rds
Ignored: output/meta-mouse-vs-human/teufel_genes.rds
Ignored: output/meta-mouse-vs-human/teufel_genes_hs.rds
Ignored: output/meta-mouse-vs-human/z_score_pca.rds
Ignored: output/mouse-acute-apap/.DS_Store
Ignored: output/mouse-acute-apap/Icon
Ignored: output/mouse-acute-apap/limma_result.rds
Ignored: output/mouse-acute-apap/meta_data.rds
Ignored: output/mouse-acute-apap/normalized_expression.rds
Ignored: output/mouse-acute-apap/pca_result.rds
Ignored: output/mouse-acute-apap/stem/.DS_Store
Ignored: output/mouse-acute-apap/stem/Icon
Ignored: output/mouse-acute-apap/stem/input/Icon
Ignored: output/mouse-acute-apap/stem/input/apap.txt
Ignored: output/mouse-acute-apap/stem/output/Icon
Ignored: output/mouse-acute-apap/stem_characterization.rds
Ignored: output/mouse-acute-apap/stem_result.rds
Ignored: output/mouse-acute-apap/z_scores.rds
Ignored: output/mouse-acute-bdl/.DS_Store
Ignored: output/mouse-acute-bdl/Icon
Ignored: output/mouse-acute-bdl/limma_result.rds
Ignored: output/mouse-acute-bdl/meta_data.rds
Ignored: output/mouse-acute-bdl/normalized_expression.rds
Ignored: output/mouse-acute-bdl/pca_result.rds
Ignored: output/mouse-acute-bdl/stem/.DS_Store
Ignored: output/mouse-acute-bdl/stem/Icon
Ignored: output/mouse-acute-bdl/stem/input/Icon
Ignored: output/mouse-acute-bdl/stem/input/bdl.txt
Ignored: output/mouse-acute-bdl/stem/output/Icon
Ignored: output/mouse-acute-bdl/stem_characterization.rds
Ignored: output/mouse-acute-bdl/stem_result.rds
Ignored: output/mouse-acute-bdl/z_scores.rds
Ignored: output/mouse-acute-ccl4/.DS_Store
Ignored: output/mouse-acute-ccl4/Icon
Ignored: output/mouse-acute-ccl4/limma_result.rds
Ignored: output/mouse-acute-ccl4/meta_data.rds
Ignored: output/mouse-acute-ccl4/normalized_expression.rds
Ignored: output/mouse-acute-ccl4/pca_result.rds
Ignored: output/mouse-acute-ccl4/stem/.DS_Store
Ignored: output/mouse-acute-ccl4/stem/Icon
Ignored: output/mouse-acute-ccl4/stem/input/Icon
Ignored: output/mouse-acute-ccl4/stem/input/ccl4.txt
Ignored: output/mouse-acute-ccl4/stem/output/Icon
Ignored: output/mouse-acute-ccl4/stem_characterization.rds
Ignored: output/mouse-acute-ccl4/stem_result.rds
Ignored: output/mouse-acute-ccl4/z_scores.rds
Ignored: output/mouse-acute-lps/Icon
Ignored: output/mouse-acute-lps/limma_result.rds
Ignored: output/mouse-acute-lps/meta_data.rds
Ignored: output/mouse-acute-lps/normalized_expression.rds
Ignored: output/mouse-acute-lps/pca_result.rds
Ignored: output/mouse-acute-lps/z_scores.rds
Ignored: output/mouse-acute-ph/.DS_Store
Ignored: output/mouse-acute-ph/Icon
Ignored: output/mouse-acute-ph/limma_result.rds
Ignored: output/mouse-acute-ph/meta_data.rds
Ignored: output/mouse-acute-ph/normalized_expression.rds
Ignored: output/mouse-acute-ph/pca_result.rds
Ignored: output/mouse-acute-ph/stem/.DS_Store
Ignored: output/mouse-acute-ph/stem/Icon
Ignored: output/mouse-acute-ph/stem/input/Icon
Ignored: output/mouse-acute-ph/stem/input/hepatec.txt
Ignored: output/mouse-acute-ph/stem/output/Icon
Ignored: output/mouse-acute-ph/stem_characterization.rds
Ignored: output/mouse-acute-ph/stem_result.rds
Ignored: output/mouse-acute-ph/z_scores.rds
Ignored: output/mouse-acute-tunicamycin/Icon
Ignored: output/mouse-acute-tunicamycin/limma_result.rds
Ignored: output/mouse-acute-tunicamycin/meta_data.rds
Ignored: output/mouse-acute-tunicamycin/normalized_expression.rds
Ignored: output/mouse-acute-tunicamycin/pca_result.rds
Ignored: output/mouse-acute-tunicamycin/z_scores.rds
Ignored: output/mouse-chronic-ccl4/.DS_Store
Ignored: output/mouse-chronic-ccl4/Icon
Ignored: output/mouse-chronic-ccl4/limma_result.rds
Ignored: output/mouse-chronic-ccl4/limma_result_hs.rds
Ignored: output/mouse-chronic-ccl4/normalized_expression.rds
Ignored: output/mouse-chronic-ccl4/pca_result.rds
Ignored: output/mouse-chronic-ccl4/stem/.DS_Store
Ignored: output/mouse-chronic-ccl4/stem/Icon
Ignored: output/mouse-chronic-ccl4/stem/input/Icon
Ignored: output/mouse-chronic-ccl4/stem/input/pure_ccl4.txt
Ignored: output/mouse-chronic-ccl4/stem/output/Icon
Ignored: output/mouse-chronic-ccl4/stem_characterization.rds
Ignored: output/mouse-chronic-ccl4/stem_result.rds
Ignored: output/mouse-chronic-ccl4/z_scores.rds
Ignored: renv/library/
Ignored: renv/staging/
Ignored: tables/Supplementary Table 1.xlsx
Ignored: tables/Supplementary Table xy consistent_genes.xlsx
Ignored: tables/Supplementary Table xy exclusive_common_genes.xlsx
Ignored: tables/Supplementary Table xy human_degs.xlsx
Ignored: tables/Supplementary Table xy stem_results.xlsx
Unstaged changes:
Modified: analysis/01-mouse-chronic-ccl4.Rmd
Modified: analysis/02-mouse-acute-apap.Rmd
Modified: analysis/03-mouse-acute-ccl4.Rmd
Modified: analysis/04-mouse-acute-ph.Rmd
Modified: analysis/05-mouse-acute-bdl.Rmd
Modified: analysis/06-mouse-acute-lps.Rmd
Modified: analysis/07-mouse-acute-tunicamycin.Rmd
Modified: analysis/08-human-diehl-nafld.Rmd
Modified: analysis/09-human-hampe13-nash.Rmd
Modified: analysis/10-human-hampe14-misc.Rmd
Modified: analysis/11-human-hoang-nafld.Rmd
Modified: analysis/12-human-ramnath-fibrosis.Rmd
Modified: analysis/13-meta-chronic-vs-acute.Rmd
Modified: analysis/14-meta-mouse-vs-human.Rmd
Modified: analysis/21-plot-chronic-vs-acute.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 | 91a5ed5 | christianholland | 2021-03-29 | polishing |
| html | 7853353 | christianholland | 2021-03-04 | Build site. |
| Rmd | 580683f | christianholland | 2021-03-04 | updated abstract |
| html | ccc7ab7 | christianholland | 2021-02-28 | Build site. |
| Rmd | 6550734 | christianholland | 2021-02-28 | wflow_publish(“analysis/index.Rmd”) |
| html | ea86074 | christianholland | 2021-02-28 | Build site. |
| Rmd | 3c62198 | christianholland | 2021-02-28 | wflow_publish(“analysis/index.Rmd”) |
| html | 1ed1723 | christianholland | 2021-02-28 | Build site. |
| Rmd | a43e07d | christianholland | 2021-02-28 | wflow_publish(“analysis/index.Rmd”) |
| html | 24c0c74 | christianholland | 2021-02-28 | Build site. |
| html | 5e36b25 | christianholland | 2021-02-28 | Build site. |
| html | 5bce71f | christianholland | 2021-02-27 | Build site. |
| html | 4b2560e | christianholland | 2021-02-27 | Build site. |
| Rmd | 4496cb5 | christianholland | 2021-02-27 | cosmetics |
| html | 801b9c1 | christianholland | 2021-02-27 | Build site. |
| Rmd | c65acdd | christianholland | 2021-02-27 | wflow_publish(c(“analysis/index.Rmd”, “analysis/plot-study-overview.Rmd”, |
| html | 3d42f16 | christianholland | 2021-02-03 | Build site. |
| html | 9c62197 | christianholland | 2021-01-07 | Build site. |
| html | 45a33e4 | christianholland | 2021-01-07 | Build site. |
| html | b4ed535 | christianholland | 2021-01-05 | Build site. |
| html | 3f4f82f | christianholland | 2021-01-05 | Build site. |
| html | ce21ef0 | christianholland | 2021-01-05 | Build site. |
| html | 0a6e6bc | christianholland | 2021-01-05 | Build site. |
| html | 45c5848 | christianholland | 2020-12-30 | Build site. |
| html | c2af37f | christianholland | 2020-12-29 | Build site. |
| html | 385ea5e | christianholland | 2020-12-28 | Build site. |
| html | 57d35bb | christianholland | 2020-12-28 | Build site. |
| html | 195c1be | christianholland | 2020-12-28 | Build site. |
| html | d8a06eb | christianholland | 2020-12-28 | Build site. |
| html | 172755d | christianholland | 2020-12-28 | Build site. |
| html | 067c933 | christianholland | 2020-12-23 | Build site. |
| html | 620ffb3 | christianholland | 2020-12-23 | Build site. |
| html | a008b54 | christianholland | 2020-12-23 | Build site. |
| html | 6b6c16a | christianholland | 2020-12-23 | Build site. |
| html | 459dd00 | christianholland | 2020-12-22 | Build site. |
| html | e864f08 | christianholland | 2020-12-22 | Build site. |
| html | 6008649 | christianholland | 2020-12-21 | Build site. |
| html | 25f0b94 | christianholland | 2020-12-21 | Build site. |
| html | 8a9b7bf | christianholland | 2020-12-20 | Build site. |
| html | 24076d2 | christianholland | 2020-12-20 | Build site. |
| html | b8af094 | christianholland | 2020-12-20 | Build site. |
| html | 6dbc304 | christianholland | 2020-12-20 | Build site. |
| html | d8ff438 | christianholland | 2020-12-20 | Build site. |
| html | e22a40b | christianholland | 2020-12-20 | Build site. |
| html | af38450 | christianholland | 2020-12-19 | Build site. |
| html | c73e126 | christianholland | 2020-12-19 | Build site. |
| html | 7bb9aab | christianholland | 2020-12-18 | Build site. |
| html | 51832b8 | christianholland | 2020-12-18 | Initial page build |
| Rmd | 16718bc | christianholland | 2020-12-18 | Start workflowr project. |
Transcriptomic cross-species analysis of chronic liver disease reveals a consistent regulation pattern between humans and mice
The results and the analysis scripts presented on this website ensures the reproducibility of all bioinformatics related findings presented in “Transcriptomic cross-species analysis of chronic liver disease reveals a consistent regulation pattern between humans and mice”. Please see below to get more information about the individual analysis and some tips on how to reproduce the results.
Abstract
Background and aims
Mouse models are frequently used to study chronic liver diseases (CLD). To assess their translational relevance, we quantified the similarity of commonly used mouse models to human CLD based on transcriptome data.
Methods
Gene expression data from 372 patients were compared to data from acute and chronic mouse models comprising 227 mice, and additionally to nine published gene sets of chronic mouse models. Genes consistently altered in humans and mice were mapped to liver cell types based on single-cell RNA-sequencing data and validated by immunostaining.
Results
Considering the top differentially expressed genes, the similarity between humans and mice varied among the mouse models and depended on the period of damage induction. The highest recall (0.4) and precision (0.33) were observed for the model with 12 months damage induction by CCl4 and by a Western type damage, respectively. Genes consistently upregulated between the chronic CCl4 model and human CLD were enriched in inflammatory and developmental processes, and mapped to cholangiocytes, macrophages, endothelial and mesenchymal cells. Downregulated genes were enriched in metabolic processes and mapped to hepatocytes. Immunostaining confirmed the regulation of selected genes and their cell type specificity. Genes that were upregulated in both acute and chronic models showed higher recall and precision with respect to human CLD than exclusively acute or chronic genes.
Conclusion
Similarly regulated genes in human and mouse CLD were identified. Despite major interspecies differences, mouse models detected 40% of the genes significantly altered in human CLD. The translational relevance of individual genes can be assessed at https://saezlab.shinyapps.io/liverdiseaseatlas/.
Analysis
The tab Mouse models contains Rmarkdown scripts to analyze and characterize the transcriptomic profiles of acute and chronic liver disease mouse models. These analyses comprised
- Normalization
- PCA analysis
- Differential gene expression analysis
- Time series clustering and characterization (if applicable)
The tab Patient cohorts contains Rmarkdown scripts to analyze and characterize the transcriptomic profiles of patient cohorts suffering from various chronic liver disease etiologies. These analyses comprised:
- Normalization
- PCA analysis
- Differential gene expression analysis
The tab Meta analysis contains Rmarkdown scripts to integrate acute and chronic mouse models with patient cohorts.
- Chronic vs. acute
- Identification of exclusively and commonly- regulated genes of chronic and acute disease in mice.
- Mouse vs. human
- Identification of consistently regulated genes in the chronic CCl4[mouse-chronic-ccl4.html] mouse model and patients.
- Quantification of the similarity of the in total 12 chronic mouse models with the different human patient cohorts based on precision and recall.
The tab Figures contains Rmarkdown scripts to generate the figures used in the manuscript.
How can I reproduce the analysis?
We have used the workflowr package to organize the analysis scripts within this project so please familiarize yourself with its concept.
- Clone the repository from https://github.com/saezlab/liver-disease-atlas which automatically provides you with all analysis scripts and the correct directory structure.
- You need to install all packages that are required for the analyses. The package renv allows you to easily install the packages with the correct versions:
install.packages("renv")
renv::restore()The GitHub repository contains only the analysis code and same small objects. All raw data is deposited at Zenodo
. Download the zipped datafolder unzip it and replace the existingdatafolder at the root level of the R-project.Run all analyses by running
install.packages("workflowr")
workflowr::wflow_build(republish = TRUE)All intermediate and final results will be saved in the output folder. Please make sure to run all analyses in the specified order as downstream analyses depend on previously generated results.
How to cite?
Holland CH, Ramirez Flores RO, Myllys M, Hassan R, Edlund K, Hofmann U, Marchan R, Cadenas C, Reinders J, Hoehme S, Seddek A, Dooley S, Keitel V, Godoy P, Begher-Tibbe B, Trautwein C, Rupp C, Mueller S, Longerich T, Hengstler JG#, Saez-Rodriguez J#, Ghallab A#. “Transcriptomic cross-species analysis of chronic liver disease reveals a consistent regulation pattern between humans and mice.” In preparation. 2021.
#Shared senior authorship
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 rstudioapi_0.13 whisker_0.4 knitr_1.30
[5] magrittr_2.0.1 R6_2.5.0 rlang_0.4.9 stringr_1.4.0
[9] tools_4.0.2 xfun_0.19 git2r_0.27.1 htmltools_0.5.0
[13] ellipsis_0.3.1 rprojroot_2.0.2 yaml_2.2.1 digest_0.6.27
[17] tibble_3.0.4 lifecycle_0.2.0 crayon_1.3.4 later_1.1.0.1
[21] vctrs_0.3.6 promises_1.1.1 fs_1.5.0 glue_1.4.2
[25] evaluate_0.14 rmarkdown_2.6 stringi_1.5.3 compiler_4.0.2
[29] pillar_1.4.7 httpuv_1.5.4 renv_0.12.3 pkgconfig_2.0.3