Last updated: 2026-04-23

Checks: 2 0

Knit directory: cf-eti-bal-scrna/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). 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

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: 902be53

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 902be53. 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:    ._.DS_Store
    Ignored:    code/._bal_RecM.integration_clustering.R
    Ignored:    data/._README.md
    Ignored:    data/AM.markers.csv
    Ignored:    data/DE/AM-CCL/CFB_vs_C/
    Ignored:    data/DE/AM-CCL/CFN_vs_C/
    Ignored:    data/DE/AM-CCL/CFN_vs_CFB/GO_BP/
    Ignored:    data/DE/AM-CCL/CFN_vs_CFB/GO_CC/
    Ignored:    data/DE/AM-CCL/CFN_vs_CFB/GO_MF/
    Ignored:    data/DE/AM-CCL/CFN_vs_CFB/Reactome/
    Ignored:    data/DE/AM-CCL/CFN_vs_CFB/WikiPathway/
    Ignored:    data/DE/Prolif M/CFB_vs_C/GO_BP/
    Ignored:    data/DE/Prolif M/CFB_vs_C/GO_CC/
    Ignored:    data/DE/Prolif M/CFB_vs_C/GO_MF/
    Ignored:    data/DE/Prolif M/CFB_vs_C/Reactome/
    Ignored:    data/DE/Prolif M/CFB_vs_C/WikiPathway/
    Ignored:    data/DE/Prolif M/CFN_vs_C/
    Ignored:    data/DE/ruv/
    Ignored:    data/Fig3A.stat.csv
    Ignored:    data/Li.stat.csv
    Ignored:    data/Liao.stat.csv
    Ignored:    data/Major.markers.csv
    Ignored:    data/Morrell.stat.csv
    Ignored:    data/Present.stat.csv
    Ignored:    data/RecM.markers.csv
    Ignored:    data/SCEs
    Ignored:    data/Wendisch.stat.csv
    Ignored:    data/cellbender
    Ignored:    data/cytokine
    Ignored:    data/plots
    Ignored:    data/sample_sheets
    Ignored:    data/vireo
    Ignored:    output/plots/combined/

Unstaged changes:
    Modified:   data/README.md

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
Rmd 902be53 tcwong1994 2026-04-23 Update index.Rmd and about.Rmd
html fb36d82 tcwong1994 2026-04-23 Build site.
Rmd c689c0a tcwong1994 2026-04-23 Update index.Rmd
html 9a73276 tcwong1994 2026-04-23 Build site.
Rmd 69aa89b tcwong1994 2026-04-23 Commit index Rmd
Rmd e9cb32b tcwong1994 2026-04-23 Commit all analysis Rmd sources
html 8ac1a7b tcwong1994 2026-04-22 Build site.
Rmd 8ca4b8f tcwong1994 2026-04-22 workflowr::wflow_publish("analysis/index.Rmd", verbose = TRUE)
html 7b2fd64 tcwong1994 2026-04-22 Publish pre-rendered workflowr HTML pages
html e13f610 tcwong1994 2026-04-22 Initialize workflowr scaffold
Rmd 8496b1d tcwong1994 2026-04-22 Start workflowr project.

Data Processing

Demultiplexing

Quality control