Last updated: 2022-04-26

Checks: 1 1

Knit directory: diamantopoulou-ctc-dynamics/

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: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Repository version: 1977b53

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 1977b53. 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: 


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    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/0_differential_expression_gsea_gsva.Rmd
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    Untracked:  analysis/patients_ctc_counts_distribution.Rmd
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Unstaged changes:
    Modified:   analysis/about.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/license.Rmd

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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 a1ff2cd fcg-bio 2022-04-25 Build site.
html 4277859 fcg-bio 2022-04-25 Build site.
Rmd d9e45e9 fcg-bio 2022-04-25 Start workflowr project.

Publication

Diamantopoulou, Z., Castro-Giner, F., Schwab F.D., Foerster C., Saini, M., Budinjas, S., Strittmatter, K., Krol, I., Seifert, B., Heinzelmann-Schwarz, V., Kurzeder, C., Rochlitz, C., Vetter, M., Weber, W.P., & Aceto N. The metastatic spread of breast cancer is accomplished during sleep time. (2022)

Abstract

We isolated live circulating tumor cells (CTCs) from a breast cancer patient (number of CTCs = 36) and two breast cancer xenografts, NSG-CDX-BR16 (number of CTCs = 138) and NSG-LM2 (number of CTCs = 108) at different time points. Isolated CTCs were categorized into three different types : single CTC, CTC clusters and CTC-white blood cells (CTC-WBC) clusters. Amplified cDNA was prepared according to the Smart-seq2 protocol. Libraries were prepared using with Nextera XT (Illumina) and sequenced on Illumina NextSeq500 instrument in 75-bp single-read mode.

Data pre-processing

Raw data is available at Gene Expression Omnibus (GEO, NCBI; accession number GSE180097). Data processing is computationally expensive and is not covered in this repository. We provide description of the data pre-processing workflow together with software version in the original publication. Processed data, large result files, additional functions, references and metadata are were archived at https://doi.org/10.5281/zenodo.6358987 .

Data and code availability

To reproduce our analysis, first clone source code from the GitHub repository

git clone https://github.com/TheAcetoLab/diamantopoulou-ctc-dynamics.git

Next, download processed data deposited in Zenodo into the cloned project folder ./data directory and untar the files.

for file in *.tar.gz; do tar xzvf "${file}" && rm "${file}"; done

Reproducibility

The results form our analyses are listed below in webpage format. They were generated from R Markdown documents deposited in the GitHub repository. The workflow of the analysis was created using the workflowr R package and can be reproduced in its totality using workflowr wflow_build command after the installation of the proper R-packages. Session info, including R and package versions, was automatically included at the end of each analysis file.

Some files containing results from differential expression or gene-set enrichment analyses were deposited in Zenodo. In order to generate those files again change the option eval = FALSE to eval = TRUE in the specific code chunk from the R Markdown file.