Last updated: 2025-05-23

Checks: 2 0

Knit directory: Lung_scMultiomics_paper/

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: 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: 007fdb9

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 007fdb9. 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: 


Untracked files:
    Untracked:  ArchRLogs/
    Untracked:  Lung_scMultiomics_paper.Rproj
    Untracked:  _workflowr.yml
    Untracked:  analysis/ArchRLogs/
    Untracked:  analysis/about.knit.md
    Untracked:  analysis/archive.Rmd
    Untracked:  analysis/figures_for_grant_application.Rmd
    Untracked:  analysis/link_peaks_to_genes.Rmd
    Untracked:  code/run_GO_enrichment.R
    Untracked:  data/p2g_res/
    Untracked:  output/u19_multiomics

Unstaged changes:
    Modified:   README.md
    Modified:   analysis/heritability_enrichment_for_lung_open_chromatin.Rmd
    Modified:   analysis/identify_cell_types.Rmd
    Modified:   analysis/identify_lung_specific_transcriptomic_features.Rmd
    Modified:   analysis/test.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 007fdb9 Jing Gu 2025-05-22 Build site.
Rmd fa91886 Jing Gu 2025-05-22 updated index page
html 497b42c Jing Gu 2025-05-14 Build site.
html 9008bd6 Jing Gu 2025-05-14 Build site.
Rmd c40f0da Jing Gu 2025-05-14 DEG analyses
html 358af12 Jing Gu 2025-05-13 Build site.
Rmd 53d9d85 Jing Gu 2025-05-13 updated index page
Rmd db6ddbb Jing Gu 2025-05-12 started workflowr
html db6ddbb Jing Gu 2025-05-12 started workflowr

Introduction

Previous study showed immune cells have a shared role in the development of both AOA and COA based on heritability analysis on ATAC-seq data of blood and lung cell types. Due to lack of resolution, it is unclear if different immune subsets sampled from lung or other tissues can have distinct roles in the genetics of asthma.

Hypotheses

Experiment design

Single-cell multiomics on paired lung and spleen samples from 9 donors (6 controls and 3 cases).

Results

annotate cell types for scMultiomics datasets

transcriptomic features specific to lung

heritability enrichment for lung open chromatin regions

linking asthma-related CREs to genes