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.

R Markdown file: up-to-date

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Repository version: 01ec959

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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    Ignored:    output/deseq2-mini_bulk4_dds.pt2-Treatment withdrawn-vs-Never treated.rds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/bulkRNA-index.Rmd) and HTML (docs/bulkRNA-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 01ec959 Javier Herrero 2021-08-16 wflow_publish(all = T)
html 01ec959 Javier Herrero 2021-08-16 wflow_publish(all = T)
html e02ea6e Javier Herrero 2021-08-16 Build site.
html cfa55c7 Javier Herrero 2021-08-16 Build site.
Rmd 6f629e4 Javier Herrero 2021-08-16 Bulk RNA pages are now complete
html 80a3f49 Javier Herrero 2021-08-16 Build site.
Rmd 1a35752 Javier Herrero 2021-08-16 Adding Bulk RNA / GSEA page
html b6f5b35 Javier Herrero 2021-08-13 Build site.
html a7a695e Javier Herrero 2021-08-13 Build site.
Rmd c2ccafd Javier Herrero 2021-08-13 Add “Bulk RNAseq / DESeq2” page
html c2ccafd Javier Herrero 2021-08-13 Add “Bulk RNAseq / DESeq2” page
Rmd 146911e Javier Herrero 2021-08-13 Adding Bulk RNAseq / PCA page
html 146911e Javier Herrero 2021-08-13 Adding Bulk RNAseq / PCA page
Rmd 42e5864 Javier Herrero 2021-08-13 Init workflowr website
html 42e5864 Javier Herrero 2021-08-13 Init workflowr website

1. PCA

This analysis is used in Figure S5A and S5B of the mss.

DESeq2 uses the top 500 most variable genes by default to draw the PCA. In this case, we are using the top 1000 genes (for historical reasons).

Generates Extended Figure 5a and Extended Figure 5b

2. Bulk RNA-seq DESeq2

This runs DESeq2 and stores the results in the output folder.

3. Bulk RNA-seq Gene Set Enrichment Analysis

This runs fGSEA and stores the results in the output folder.

Generates Figure 5c

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