Last updated: 2021-08-18

Checks: 1 1

Knit directory: SCENIC_pipeline/

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.


The R Markdown is untracked by Git. 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.

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 8e02d7f. 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
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store

Untracked files:
    Untracked:  analysis/Overview_of_SCENIC_workflow.Rmd
    Untracked:  analysis/Step0_Data_preparation.Rmd
    Untracked:  analysis/Step0_Installation_of_packages.Rmd
    Untracked:  analysis/Step1_GENIE3_identification_of-potential_TF-targets_based_on_co-expression.Rmd
    Untracked:  analysis/Step2_motif_discovery.Rmd
    Untracked:  analysis/Step3_Cell_scoring.Rmd
    Untracked:  analysis/Step4_Clustering.Rmd
    Untracked:  analysis/images/
    Untracked:  analysis/related_conceptions.Rmd
    Untracked:  images/

Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   analysis/index.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.


There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.


  1. module:一个转录因子TF和其相应的预测靶基因targets构成一个module。
  2. co-expression module/network:基于表达数据得到的共表达关系,量化指标可以为pearson correlation coefficient
  3. regulon: In cell biology and genetics, a regulon is a collection of genes or operons under regulation by the same regulatory protein.在细胞生物学和遗传学中个,调节子指的是受同一个调控蛋白调控的基因或操纵子的集合。 在该分析中指的是:每个TF及其potential direct targets构成一个regulon(可翻译成调控单元)。
  4. GRN, gene regulatory network 基因调控网络: