Last updated: 2025-12-19

Checks: 2 0

Knit directory: fsusie-experiments/analysis/

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: de24cf8

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 de24cf8. 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:  analysis/rosmap_h3k27ac_cache/
    Untracked:  analysis/rosmap_overview_cache/
    Untracked:  data/afreq.RData
    Untracked:  data/analysis_result/Fungen_xQTL.ENSG00000163808.cis_results_db.export.rds
    Untracked:  data/analysis_result/ROSMAP_haQTL.chr3_43915257_48413435.fsusie_mixture_normal_top_pc_weights.rds
    Untracked:  data/analysis_result/ROSMAP_mQTL.chr3_43915257_48413435.fsusie_mixture_normal_top_pc_weights.rds
    Untracked:  outputs/CD2AP_obj.RData
    Untracked:  outputs/CR1_CR2_all_effects.RData
    Untracked:  outputs/CR1_CR2_obj.RData
    Untracked:  outputs/ROSMAP_DLPFC_mega_eQTL.cs_only.tsv.gz
    Untracked:  outputs/ROSMAP_DLPFC_pQTL.cs_only.tsv.gz
    Untracked:  outputs/ROSMAP_haQTL_cs_effect_ha_peak_annotation.tsv.gz
    Untracked:  outputs/ROSMAP_haQTL_cs_snp_annotation.tsv.gz
    Untracked:  outputs/ROSMAP_haQTL_cs_snp_toppc1_annotation.tsv.gz
    Untracked:  outputs/ROSMAP_mQTL_cs_effect_cpg_annotation.tsv.gz
    Untracked:  outputs/ROSMAP_mQTL_cs_snp_annotation.tsv.gz
    Untracked:  outputs/ROSMAP_mQTL_cs_snp_toppc1_annotation.tsv.gz

Unstaged changes:
    Modified:   analysis/whitening_demo.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
Rmd de24cf8 Peter Carbonetto 2025-12-19 wflow_publish("index.Rmd")
html a4f57c0 Peter Carbonetto 2025-05-13 Updated the overview page.
Rmd c9134cc Peter Carbonetto 2025-05-13 wflow_publish("index.Rmd")
html eb94ec6 Peter Carbonetto 2025-05-12 Added link to overview page.
Rmd 0959174 Peter Carbonetto 2025-05-12 workflowr::wflow_publish("index.Rmd", verbose = TRUE)
html ced74c2 Peter Carbonetto 2025-05-12 Build site.
Rmd 6c93429 Peter Carbonetto 2025-05-12 workflowr::wflow_publish("index.Rmd", verbose = TRUE)
html 17806bb Peter Carbonetto 2025-04-30 Build site.
Rmd 8a4d3fb Peter Carbonetto 2025-04-30 workflowr::wflow_publish("index.Rmd")
html 0b58356 Peter Carbonetto 2024-04-25 Added link to home overview page.
Rmd 23125cd Peter Carbonetto 2024-04-25 wflow_publish("analysis/index.Rmd", verbose = TRUE, view = FALSE)
html 0e8d026 Peter Carbonetto 2024-03-05 Build site.
Rmd 38ac2ce Peter Carbonetto 2024-03-05 A few fixes to the workflowr setup.
Rmd 934f9e1 Peter Carbonetto 2024-03-05 Start workflowr project.