Last updated: 2025-05-23
Checks: 2 0
Knit directory: CosMx_pipeline_LGA/
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 51b3104. 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: .Rproj.user/
Ignored: NBClust-Plots/
Ignored: analysis/figure/
Ignored: data/flatFiles/CoronalHemisphere/Run1000_S1_Half_exprMat_file.csv
Ignored: data/flatFiles/CoronalHemisphere/Run1000_S1_Half_fov_positions_file.csv
Ignored: data/flatFiles/CoronalHemisphere/Run1000_S1_Half_metadata_file.csv
Ignored: output/processed_data/Log/
Ignored: output/processed_data/RC/
Ignored: output/processed_data/SCT/
Ignored: output/processed_data/exprMat_unfiltered.RDS
Ignored: output/processed_data/fov_positions_unfiltered.RDS
Ignored: output/processed_data/metadata_unfiltered.RDS
Ignored: output/processed_data/negMat_unfiltered.RDS
Ignored: output/processed_data/seu_filtered.RDS
Ignored: output/processed_data/seu_semifiltered.RDS
Untracked files:
Untracked: analysis/images/
Unstaged changes:
Modified: analysis/_site.yml
Modified: output/performance_reports/0.0_data_loading_PR.csv
Modified: output/performance_reports/1.0_qc_and_filtering_PR.csv
Modified: output/performance_reports/2.0_normalization_PR.csv
Modified: output/performance_reports/3.0_dimensional_reduction_PR.csv
Modified: output/performance_reports/4.0_insitutype_cell_typing_PR.csv
Modified: output/performance_reports/4.1_insitutype_unsup_clustering_PR.csv
Modified: output/performance_reports/4.2_seurat_unsup_clustering_PR.csv
Modified: output/performance_reports/5.0_RC_normalization_PR.csv
Modified: output/performance_reports/5.1_RC_dimensional_reduction_PR.csv
Modified: output/performance_reports/6.0_Log_normalization_PR.csv
Modified: output/performance_reports/6.1_Log_dimensional_reduction_PR.csv
Modified: output/performance_reports/pipeline_PR.csv
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/license.Rmd
) and HTML
(docs/license.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 | 51b3104 | lidiaga | 2025-05-23 | Build site. |
html | 8a9f079 | lidiaga | 2025-05-20 | Build site. |
Rmd | cf77662 | lidiaga | 2025-05-19 | Edit website files |
Rmd | 0065eb1 | lidiaga | 2025-05-17 | Start workflowr project. |
All code in this repository is licensed under the MIT License.
You can view the full license text by visiting choosealicense.com/licenses/mit.
All written content on this site is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) license. For more details, see the Creative Commons summary or read the full legal code.
If you use or reference this work in academic or technical materials, please cite it as follows: