Last updated: 2023-04-17
Checks: 1 1
Knit directory:
~/projects/lung_immune_fine_mapping/
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.
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.
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 b52834c. 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: .ipynb_checkpoints/
Ignored: analysis/annotate_clusters.nb.html
Ignored: analysis/data_QC.nb.html
Ignored: output/DE_analysis_mast_Tsub/
Untracked files:
Untracked: README.html
Untracked: analysis/.ipynb_checkpoints/
Untracked: analysis/annotate_clusters.Rmd
Untracked: analysis/data_QC.Rmd
Untracked: analysis/lung_immune_fine_mapping.Rproj
Untracked: analysis/notebooks/
Untracked: analysis/peak_characterization.Rmd
Untracked: analysis/quality_control.Rmd
Untracked: code/.ipynb_checkpoints/
Untracked: code/learn_best_practices_in_R.r
Untracked: code/run_DE_under_null.r
Untracked: output/.ipynb_checkpoints/
Untracked: output/DA_analysis_LR/
Untracked: output/DA_analysis_LR_covariate/
Untracked: output/DA_peaks_nearby_genes.csv
Untracked: output/DEG_T_subsets_by_celltype_heatmap.pdf
Untracked: output/DEG_Tsub_by_celltype_heatmap.pdf
Untracked: output/DEG_merged_by_celltype_heatmap.pdf
Untracked: output/DE_across_celltypes/
Untracked: output/DE_analysis_mast/
Untracked: output/DE_analysis_mast_minpct_0.25/
Untracked: output/DE_analysis_wilcox/
Untracked: output/DE_analysis_wilcox_Tsub/
Untracked: output/all_merged_metadata.txt
Untracked: output/history/
Unstaged changes:
Modified: analysis/index.Rmd
Deleted: lung_immune_fine_mapping.Rproj
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 | a747e1b | Jing Gu | 2023-04-04 | add motif enrichment analyses |
| html | 3210eeb | Jing Gu | 2023-03-24 | differential accessibility analysis |
| html | a62518c | Jing Gu | 2023-01-19 | Build site. |
| html | 75f6c39 | Jing Gu | 2023-01-19 | Build site. |
| Rmd | 1acc8b6 | Jing Gu | 2023-01-19 | wflow_publish(c("analysis/index.Rmd")) |
| html | 954cb2a | Jing Gu | 2023-01-19 | perform DE analysis |
| html | fe87999 | Jing Gu | 2022-12-29 | Build site. |
| Rmd | 2003997 | Jing Gu | 2022-12-29 | Publish README.Rmd |
| html | 9117390 | Jing Gu | 2022-12-29 | Build site. |
| Rmd | e475baf | Jing Gu | 2022-12-29 | Publish README.Rmd |
| html | c864f9e | Jing Gu | 2022-12-29 | Build site. |
| html | 48e445a | Jing Gu | 2022-12-29 | Build site. |
| Rmd | b89c4ae | Jing Gu | 2022-12-29 | Start workflowr project. |
This project is about using functional profiling of lung immune cells to better understand the genetics of asthma and allergy diseases.
TBD
Click here for downloading the PPT and data tables