Last updated: 2024-05-21

Checks: 1 1

Knit directory: PPP/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). 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: 3e0915c

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 3e0915c. 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

Untracked files:
    Untracked:  data/aracne.networks.csv

Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   analysis/index.Rmd
    Modified:   analysis/viper.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
html 3e0915c Zhen Zuo 2024-05-21 Build site.
Rmd b4440e6 Zhen Zuo 2024-05-21 wflow_git_commit(all = TRUE)
html 0fa724b Zhen Zuo 2024-05-21 Publish the initial files for myproject
html 4aa2e51 Zhen Zuo 2024-05-21 Build site.
Rmd 8aa49f1 Zhen Zuo 2024-05-21 Start workflowr project.

Welcome to my research website.

Click on this link to see my results.

Environment setup

Set up python2.7

To set up python2.7 on MacOs

Then run

conda create -n py27 --f py27.yml

To active it

source /opt/homebrew/Caskroom/mambaforge/base/etc/profile.d/conda.sh;  
conda activate py27;
Set up Viper 
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("viper")