Last updated: 2021-08-16

Checks: 2 0

Knit directory: Turati_NatCancer_2021/

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! 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 9254340. 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:    bulkRNA/
    Ignored:    data/bulk4_counts.rda
    Ignored:    data/bulk4_dds.rda
    Ignored:    data/paper_palette.rda
    Ignored:    data/signatures.rda
    Ignored:    output/deseq2-mini_bulk4_dds.3pts-Treated-vs-Untreated.rds
    Ignored:    output/deseq2-mini_bulk4_dds.pt1-Treated-vs-Untreated.rds
    Ignored:    output/deseq2-mini_bulk4_dds.pt12-Treated-vs-Untreated.rds
    Ignored:    output/deseq2-mini_bulk4_dds.pt13-Treated-vs-Untreated.rds
    Ignored:    output/deseq2-mini_bulk4_dds.pt2-Acutely treated-vs-Chronically treated.rds
    Ignored:    output/deseq2-mini_bulk4_dds.pt2-Acutely treated-vs-Never treated.rds
    Ignored:    output/deseq2-mini_bulk4_dds.pt2-Chronically treated-vs-Never treated.rds
    Ignored:    output/deseq2-mini_bulk4_dds.pt2-Relapse-vs-Never treated.rds
    Ignored:    output/deseq2-mini_bulk4_dds.pt2-Treatment withdrawn-vs-Never treated.rds
    Ignored:    output/fgsea_results.RDS
    Ignored:    output/figures/ExtFig5a_pca_3patients.pdf
    Ignored:    output/figures/ExtFig5b_pca_treatment_response.pdf
    Ignored:    output/figures/Fig5C_fgsea_selected_signatures.pdf
    Ignored:    output/figures/ItemS2.pdf
    Ignored:    output/tables/ExtFig5a_bulkRNAseq_data.xlsx
    Ignored:    output/tables/ExtFig5b_bulkRNAseq_data.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/about.Rmd) and HTML (docs/about.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 b6f5b35 Javier Herrero 2021-08-13 Build site.
html 537463a Javier Herrero 2021-08-13 Update site
Rmd 42e5864 Javier Herrero 2021-08-13 Init workflowr website
html 42e5864 Javier Herrero 2021-08-13 Init workflowr website

Data were generated by Virginia Turati in Tariq Enver’s lab.

Single cell mutation calling was perfomed by Lucia Conde.

Single cell WGS normalisation and segmentation was performed by Chuling Ding.

Initial bulk RNA-seq were analysed by John Ambrose.

Most analyses of the bulk and single cell RNA-seq data (including exploratory analyses) were performed by Afonso Guerra.

Some additional analyses were performed by Chela James and Javier Herrero.

Methylation data were processed ana analysed by Simone Ecker in Stephan Beck’s lab.

Re-packaging and re-organisation of the code and data was performed by Javier Herrero.

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