Last updated: 2018-09-21

workflowr checks: (Click a bullet for more information)

  • ✔ R Markdown file: up-to-date

    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.

  • ✔ Repository version: 283f43b

    Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

    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/

Unstaged changes:
    Deleted:    analysis/snp2net_liver.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.
Expand here to see past versions:
    File Version Author Date Message
    Rmd 283f43b Xiang Zhu 2018-09-21 wflow_publish(“analysis/index.Rmd”)
    html f4e42f1 Xiang Zhu 2018-09-20 Build site.
    Rmd 69cfef7 Xiang Zhu 2018-09-20 wflow_publish(“analysis/index.Rmd”)
    html c08d574 Xiang Zhu 2018-09-19 Build site.
    Rmd 3a196a1 Xiang Zhu 2018-09-19 wflow_publish(“analysis/index.Rmd”)
    html b303bb7 Xiang Zhu 2018-09-04 Build site.
    Rmd 665f7a3 Xiang Zhu 2018-09-04 wflow_publish(“analysis/index.Rmd”)
    html 2a3e63f Xiang Zhu 2018-08-30 Build site.
    Rmd a5d1757 Xiang Zhu 2018-08-30 wflow_publish(“analysis/index.Rmd”)
    html 6142cc2 Xiang Zhu 2018-07-24 Build site.
    Rmd d17ed5f Xiang Zhu 2018-07-24 wflow_publish(“analysis/index.Rmd”)
    html b978776 Xiang Zhu 2018-07-24 Build site.
    Rmd 1017c63 Xiang Zhu 2018-07-24 wflow_publish(“analysis/index.Rmd”)
    html 9aaa70f Xiang Zhu 2018-07-19 Build site.
    Rmd 2cd97ad Xiang Zhu 2018-07-19 wflow_publish(“analysis/index.Rmd”)
    html 889612b Xiang Zhu 2018-07-19 Build site.
    html fcdb217 Xiang Zhu 2018-07-19 Build site.
    Rmd 041a3ef Xiang Zhu 2018-07-19 wflow_publish(files = c(“analysis/index.Rmd”, “analysis/license.Rmd”))
    Rmd c07849b Xiang Zhu 2018-07-19 Start workflowr project.

If you have any question about this project, please feel free to contact me: Xiang Zhu, xiangzhu@stanford.edu.

Software development

Data analysis

Likelihood ratio assessments

Below are some quick assessments of PECA networks I received from Duren, using a simple likelihood ratio calculation introduced in Zhu and Stephens (2017). The aim of these quick assessments is to confirms whether these networks are informative in identifying disease-related tissues or cell types.

Application of new methods

Below are applications of the new methods to real datasets.

This reproducible R Markdown analysis was created with workflowr 1.1.1