Last updated: 2024-07-26
Checks: 7 0
Knit directory: Cinquina_2024/
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 job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20240320) was run prior to running
the code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
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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 373fd42. 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/
Ignored: data/SCP1290/
Ignored: data/azimuth_integrated.rds
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 | 285dc11 | Evgenii O. Tretiakov | 2024-07-26 | update theme in Rmds |
| html | 1d9d8ea | Evgenii O. Tretiakov | 2024-07-26 | Build site. |
| Rmd | 25c1972 | Evgenii O. Tretiakov | 2024-07-25 | fix typos |
| html | 25c1972 | Evgenii O. Tretiakov | 2024-07-25 | fix typos |
| Rmd | 78f7fe4 | Evgenii O. Tretiakov | 2024-07-25 | add description |
| html | d69bcf7 | EugOT | 2024-03-20 | fix .gitignore |
| Rmd | fbebf81 | EugOT | 2024-03-20 | Start workflowr project. |
Welcome to the analysis website for the manuscript “Astrocytes modulate neuronal development by S100A6 signaling”. This site contains the code and detailed methods used in our study.
To reproduce the analysis environment, pull the Docker image using:
docker pull etretiakov/workbench-session-complete:jammy-2024.06.19-custom-12.8Typical pull time on a standard desktop computer with good internet connection should be within 30 minutes
workflowr::wflow_publish(
c(
"analysis/cortex_visualisation.Rmd",
"analysis/MTT.Rmd"
),
message = "Reproduce analysis site",
project = "."
)This command will:
project = ".").Make sure to run this command from within your Docker container to ensure all dependencies are available. You may need to adjust the file paths if your R Markdown files are located in a different directory within your project structure.
For any questions or issues, please open an issue on the GitHub repository.
sessionInfo()R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] jsonlite_1.8.8 compiler_4.4.0 promises_1.3.0 Rcpp_1.0.12
[5] stringr_1.5.1 git2r_0.33.0 callr_3.7.6 later_1.3.2
[9] jquerylib_0.1.4 yaml_2.3.8 fastmap_1.2.0 here_1.0.1
[13] R6_2.5.1 knitr_1.47 tibble_3.2.1 rprojroot_2.0.4
[17] bslib_0.7.0 pillar_1.9.0 rlang_1.1.4 utf8_1.2.4
[21] cachem_1.1.0 stringi_1.8.4 httpuv_1.6.15 xfun_0.45
[25] getPass_0.2-4 fs_1.6.4 sass_0.4.9 cli_3.6.2
[29] magrittr_2.0.3 ps_1.7.6 digest_0.6.35 processx_3.8.4
[33] rstudioapi_0.16.0 lifecycle_1.0.4 vctrs_0.6.5 evaluate_0.24.0
[37] glue_1.7.0 whisker_0.4.1 fansi_1.0.6 rmarkdown_2.27
[41] httr_1.4.7 tools_4.4.0 pkgconfig_2.0.3 htmltools_0.5.8.1