Last updated: 2024-07-04

Checks: 2 0

Knit directory: KODAMA-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.


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.

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 62ada19. 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:


Unstaged changes:
    Deleted:    .DS_Store
    Deleted:    KODAMA-Analysis.Rproj
    Modified:   MERFISH.Rmd
    Deleted:    README.md
    Deleted:    _workflowr.yml
    Deleted:    analysis/DLPFC.Rmd
    Deleted:    analysis/MERFISH.Rmd
    Deleted:    analysis/Prostate.Rmd
    Deleted:    analysis/STARmap.Rmd
    Deleted:    analysis/VisiumHD.Rmd
    Deleted:    analysis/_site.yml
    Deleted:    analysis/about.Rmd
    Deleted:    analysis/index.Rmd
    Deleted:    analysis/license.Rmd
    Deleted:    analysis/simulation.Rmd
    Deleted:    code/Prostate_download.sh
    Deleted:    code/Prostate_preprocessing.R
    Deleted:    code/README.md
    Deleted:    data/.gitattributes
    Deleted:    data/Moffitt_and_Bambah-Mukku_et_al_merfish_all_cells.csv
    Deleted:    data/Prostate_data.RData
    Deleted:    data/README.md
    Deleted:    data/merfish.Rmd
    Deleted:    data/vis.R
    Deleted:    docs/.DS_Store
    Deleted:    docs/.nojekyll
    Deleted:    docs/DLPFC.html
    Deleted:    docs/MERFISH.html
    Deleted:    docs/Prostate.html
    Deleted:    docs/STARmap.html
    Deleted:    docs/VisiumHD.html
    Deleted:    docs/about.html
    Deleted:    docs/figure/MERFISH.Rmd/unnamed-chunk-5-1.png
    Deleted:    docs/figure/MERFISH.Rmd/unnamed-chunk-5-2.png
    Deleted:    docs/figure/Prostate.Rmd/unnamed-chunk-1-1.png
    Deleted:    docs/figure/simulation.Rmd/unnamed-chunk-1-1.png
    Deleted:    docs/figure/simulation.Rmd/unnamed-chunk-2-1.png
    Deleted:    docs/index.html
    Deleted:    docs/license.html
    Deleted:    docs/simulation.html
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css.map
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/bootstrap.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/bootstrap.css.map
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/bootstrap.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/cerulean.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/cosmo.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/darkly.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/flatly.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/Lato.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/LatoBold.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/LatoItalic.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/NewsCycle.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/NewsCycleBold.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSans.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSansBold.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSansBoldItalic.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSansItalic.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSansLight.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/OpenSansLightItalic.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/Raleway.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/RalewayBold.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/Roboto.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/RobotoBold.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/RobotoLight.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/RobotoMedium.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/SourceSansPro.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/SourceSansProBold.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/SourceSansProItalic.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/SourceSansProLight.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/fonts/Ubuntu.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/journal.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/lumen.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/paper.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/readable.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/sandstone.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/simplex.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/spacelab.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/united.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/css/yeti.min.css
    Deleted:    docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.eot
    Deleted:    docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.svg
    Deleted:    docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.ttf
    Deleted:    docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff
    Deleted:    docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff2
    Deleted:    docs/site_libs/bootstrap-3.3.5/js/bootstrap.js
    Deleted:    docs/site_libs/bootstrap-3.3.5/js/bootstrap.min.js
    Deleted:    docs/site_libs/bootstrap-3.3.5/js/npm.js
    Deleted:    docs/site_libs/bootstrap-3.3.5/shim/html5shiv.min.js
    Deleted:    docs/site_libs/bootstrap-3.3.5/shim/respond.min.js
    Deleted:    docs/site_libs/font-awesome-6.4.2/css/all.css
    Deleted:    docs/site_libs/font-awesome-6.4.2/css/all.min.css
    Deleted:    docs/site_libs/font-awesome-6.4.2/css/v4-shims.css
    Deleted:    docs/site_libs/font-awesome-6.4.2/css/v4-shims.min.css
    Deleted:    docs/site_libs/font-awesome-6.4.2/webfonts/fa-brands-400.ttf
    Deleted:    docs/site_libs/font-awesome-6.4.2/webfonts/fa-brands-400.woff2
    Deleted:    docs/site_libs/font-awesome-6.4.2/webfonts/fa-regular-400.ttf
    Deleted:    docs/site_libs/font-awesome-6.4.2/webfonts/fa-regular-400.woff2
    Deleted:    docs/site_libs/font-awesome-6.4.2/webfonts/fa-solid-900.ttf
    Deleted:    docs/site_libs/font-awesome-6.4.2/webfonts/fa-solid-900.woff2
    Deleted:    docs/site_libs/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf
    Deleted:    docs/site_libs/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2
    Deleted:    docs/site_libs/header-attrs-2.26/header-attrs.js
    Deleted:    docs/site_libs/header-attrs-2.27/header-attrs.js
    Deleted:    docs/site_libs/highlightjs-9.12.0/default.css
    Deleted:    docs/site_libs/highlightjs-9.12.0/highlight.js
    Deleted:    docs/site_libs/highlightjs-9.12.0/textmate.css
    Deleted:    docs/site_libs/jquery-3.6.0/jquery-3.6.0.js
    Deleted:    docs/site_libs/jquery-3.6.0/jquery-3.6.0.min.js
    Deleted:    docs/site_libs/jquery-3.6.0/jquery-3.6.0.min.map
    Deleted:    docs/site_libs/jqueryui-1.13.2/AUTHORS.txt
    Deleted:    docs/site_libs/jqueryui-1.13.2/LICENSE.txt
    Deleted:    docs/site_libs/jqueryui-1.13.2/images/ui-icons_444444_256x240.png
    Deleted:    docs/site_libs/jqueryui-1.13.2/images/ui-icons_555555_256x240.png
    Deleted:    docs/site_libs/jqueryui-1.13.2/images/ui-icons_777620_256x240.png
    Deleted:    docs/site_libs/jqueryui-1.13.2/images/ui-icons_777777_256x240.png
    Deleted:    docs/site_libs/jqueryui-1.13.2/images/ui-icons_cc0000_256x240.png
    Deleted:    docs/site_libs/jqueryui-1.13.2/images/ui-icons_ffffff_256x240.png
    Deleted:    docs/site_libs/jqueryui-1.13.2/index.html
    Deleted:    docs/site_libs/jqueryui-1.13.2/jquery-ui.css
    Deleted:    docs/site_libs/jqueryui-1.13.2/jquery-ui.js
    Deleted:    docs/site_libs/jqueryui-1.13.2/jquery-ui.min.css
    Deleted:    docs/site_libs/jqueryui-1.13.2/jquery-ui.min.js
    Deleted:    docs/site_libs/jqueryui-1.13.2/jquery-ui.structure.css
    Deleted:    docs/site_libs/jqueryui-1.13.2/jquery-ui.structure.min.css
    Deleted:    docs/site_libs/jqueryui-1.13.2/jquery-ui.theme.css
    Deleted:    docs/site_libs/jqueryui-1.13.2/jquery-ui.theme.min.css
    Deleted:    docs/site_libs/navigation-1.1/codefolding-lua.css
    Deleted:    docs/site_libs/navigation-1.1/codefolding.js
    Deleted:    docs/site_libs/navigation-1.1/sourceembed.js
    Deleted:    docs/site_libs/navigation-1.1/tabsets.js
    Deleted:    docs/site_libs/tocify-1.9.1/jquery.tocify.css
    Deleted:    docs/site_libs/tocify-1.9.1/jquery.tocify.js
    Deleted:    output/README.md

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 (DLPFC.Rmd) and HTML (../docs/DLPFC.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 62ada19 Stefano Cacciatore 2024-07-04 Ajout des fichiers rmd, html, yml, etc.

Describe your project.