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.

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: 51b3104

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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/about.Rmd) and HTML (docs/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 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.

My name is Lidia Getino Álvarez, a biotechnologist with a professional career in the pharmaceutical industry and a growing interest for data science and bioinformatics.

I created this website to complement and summarize the final project of my Master’s in Bioinformatics and Biostatistics of Universitat Oberta de Catalunya: “Implementation of a bioinformatics pipeline for the analysis of spatial transcriptomics data”.

For more information, doubts or suggestions, you can view the source code and materials on the GitHub repo linked above, or contact me through my LinkedIn page here.