About

Last updated: 2024-01-01

Checks: 2 0

Knit directory: mage_2020_marker-gene-benchmarking/

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: 2632193

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 2632193. 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:    .Renviron
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    .snakemake/
    Ignored:    NSForest/.Rhistory
    Ignored:    NSForest/NS-Forest_v3_Extended_Binary_Markers_Supplmental.csv
    Ignored:    NSForest/NS-Forest_v3_Full_Results.csv
    Ignored:    NSForest/NSForest3_medianValues.csv
    Ignored:    NSForest/NSForest_v3_Final_Result.csv
    Ignored:    NSForest/__pycache__/
    Ignored:    NSForest/data/
    Ignored:    RankCorr/picturedRocks/__pycache__/
    Ignored:    benchmarks/
    Ignored:    config/
    Ignored:    data/cellmarker/
    Ignored:    data/downloaded_data/
    Ignored:    data/expert_annotations/
    Ignored:    data/expert_mgs/
    Ignored:    data/raw_data/
    Ignored:    data/real_data/
    Ignored:    data/sim_data/
    Ignored:    data/sim_mgs/
    Ignored:    data/special_real_data/
    Ignored:    figures/
    Ignored:    logs/
    Ignored:    results/
    Ignored:    weights/

Unstaged changes:
    Deleted:    analysis/expert-mgs-direction.Rmd
    Modified:   smash-fork

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/about.Rmd) and HTML (public/about.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	fcecf65	Jeffrey Pullin	2022-09-09	Build site.
html	af96b34	Jeffrey Pullin	2022-08-30	Build site.
html	0e47874	Jeffrey Pullin	2022-05-04	Build site.
html	b5045c1	Jeffrey Pullin	2022-05-02	Build site.
Rmd	048156f	Jeffrey Pullin	2022-05-02	Tweak analysis outputs
html	048156f	Jeffrey Pullin	2022-05-02	Tweak analysis outputs
html	8b989e1	Jeffrey Pullin	2022-05-02	Build site.
html	0548273	Jeffrey Pullin	2022-05-02	Build site.
html	50bca7c	Jeffrey Pullin	2022-05-02	workflowr::wflow_publish(all = TRUE, republish = TRUE)
html	ca82ce0	Jeffrey Pullin	2021-02-16	Build site.
html	2863555	Jeffrey Pullin	2021-02-10	Build site.
Rmd	1ad9d6d	Jeffrey Pullin	2021-02-10	Add workflowr website
Rmd	7971ea2	Jeffrey Pullin	2020-10-25	Initial commit

The code underlying this project is complex and running it is computationally intensive. Despite this, the project should be reproducible and even extendable with minimal effort. Find below a description of the key steps needed to reproduce the results. In the near future this process will be substantially streamlined.