Last updated: 2025-09-03

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.


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The results in this page were generated with repository version cc8470c. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    NBClust-Plots/
    Ignored:    analysis/.Rhistory
    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

Unstaged changes:
    Modified:   CosMx_pipeline_LGA.Rproj
    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
    Deleted:    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 43970ac lga-uoc 2025-09-02 Build site.
Rmd 9bc387c lga-uoc 2025-09-02 Fix navbar in About and License
Rmd 1cf5794 lga-uoc 2025-09-02 Edit website files
Rmd ee0d521 lga-uoc 2025-09-02 Start workflowr project.

Hi! I can’t introduce myself here as this is an anonymized version of the original website I created 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”.