scMR

Last updated: 2022-11-30

Checks: 2 0

Knit directory: SingleCellMR/

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: 55d887a

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 55d887a. 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:    analysis/downstream.nb.html
    Ignored:    analysis/figures.nb.html

Untracked files:
    Untracked:  analysis/DOWNSTREAM_RESULTS.Rmd
    Untracked:  analysis/eQTL_analysis.Rmd
    Untracked:  colossus/
    Untracked:  data/COLOC_MR_RESULTS/
    Untracked:  data/EXT_DATASETS/
    Untracked:  data/FIGURES/
    Untracked:  data/GWAS_STUDIES/
    Untracked:  data/MARKDOWN/
    Untracked:  data/METADATA/
    Untracked:  data/TABLES/
    Untracked:  data/derby.log
    Untracked:  data/eQTL_RESULTS/
    Untracked:  data/helper_files/
    Untracked:  data/logs/
    Untracked:  derby.log
    Untracked:  logs/

Unstaged changes:
    Modified:   analysis/_site.yml

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	55d887a	Alexander Haglund	2022-11-30	wflow_publish(c("analysis/index.Rmd"))
html	19235a0	Alexander Haglund	2022-11-30	Build site.
Rmd	1820563	Alexander Haglund	2022-11-30	wflow_publish(c("analysis/index.Rmd"))
html	597c47b	Alexander Haglund	2022-11-18	Build site.
html	8f071f3	Alexander Haglund	2022-11-18	Build site.
Rmd	38a3835	Alexander Haglund	2022-11-18	wflow_publish(c("analysis/index.Rmd", "analysis/figures.Rmd"))
Rmd	99bd48e	Alexander Haglund	2022-11-10	Start workflowr project.

This website contains all code in the paper; “Single-cell Mendelian randomisation identifies cell-type specific genetic effects on human brain disease and behaviour”