Last updated: 2023-10-27

Checks: 2 0

Knit directory: analysis_pipelines/

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: d3e347a

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 d3e347a. 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:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/test_sldsc_splicingAnnot.Rmd
    Untracked:  code/compute_ldscore_generic_annot.sbatch
    Untracked:  code/extract_baselineLD_generic_annot.R
    Untracked:  code/ldsc_make_binary_annot_compute_ldscores_bedfiles.sbatch
    Untracked:  code/make_ldsc_binary_annots_from_bedfiles.R
    Untracked:  code/sldsc_annot_generic_baselineLD_separate.sbatch
    Untracked:  scripts/tmp.R

Unstaged changes:
    Modified:   analysis/mapgen_torus_enrichment_heart_atlas.Rmd
    Modified:   analysis/sldsc_example_GTEx_QTLs.Rmd
    Modified:   analysis/sldsc_pipeline.Rmd
    Modified:   code/extract_baselineLDv2.2_generic_annot.R
    Modified:   code/mapgen_trackplots.R
    Modified:   scripts/run_finemapping.R

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 d3e347a kevinlkx 2023-10-27 wflow_publish("analysis/index.Rmd")
html e1dd4fd kevinlkx 2023-10-20 Build site.
Rmd 86f4601 kevinlkx 2023-10-20 wflow_publish("analysis/index.Rmd")
html a065c8d kevinlkx 2022-08-18 Build site.
Rmd 84247b7 kevinlkx 2022-08-18 added link to mapgen trackplot example
html d41fa3c kevinlkx 2022-05-20 Build site.
Rmd ed628ca kevinlkx 2022-05-20 added a tutorial for AF finemapping
html cef0989 kevinlkx 2022-04-19 Build site.
Rmd 818b411 kevinlkx 2022-04-19 added TORUS enrichment analysis example with heart atlas data
html 77ce960 kevinlkx 2020-07-08 Build site.
Rmd 904f07e kevinlkx 2020-07-08 wflow_publish("analysis/index.Rmd")
html 885e012 kevinlkx 2020-07-07 Build site.
html 8468157 kevinlkx 2020-07-07 Build site.
Rmd 12bb8c3 kevinlkx 2020-07-07 wflow_publish("analysis/index.Rmd")
html 0f4a0bc kevinlkx 2020-05-25 Build site.
Rmd c6bd415 kevinlkx 2020-05-25 wflow_publish("analysis/index.Rmd")
html d5cee1f kevinlkx 2020-05-24 Build site.
html 83ec764 kevinlkx 2020-05-24 Build site.
html 28ab0ae kevinlkx 2020-05-24 Build site.
Rmd 152e4bc kevinlkx 2020-05-24 wflow_publish("analysis/index.Rmd")
html 26a2c8e kevinlkx 2020-05-24 Build site.
Rmd 6fa261f kevinlkx 2020-05-24 wflow_publish("analysis/index.Rmd")
html 40604e8 kevinlkx 2020-05-24 Build site.
Rmd 244a3a4 kevinlkx 2020-05-24 Publish the initial files for myproject
Rmd 7600104 kevinlkx 2020-05-24 Start workflowr project.

GWAS summary statistics

LDSC

TWAS

Mapgen