Last updated: 2025-05-23

Checks: 2 0

Knit directory: CosMx_pipeline_LGA/

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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

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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.

License

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Citation

If you use or reference this work in academic or technical materials, please cite it as follows:

Getino-Álvarez, L. Implementación de un pipeline bioinformático para análisis de datos de Spatial Transcriptomics. GitHub repository, [URL]. Accessed on [Date].