CosMx SMI Dataset

Last updated: 2025-05-23

Checks: 2 0

Knit directory: CosMx_pipeline_LGA/

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R Markdown file: up-to-date

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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.

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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

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/dataset.Rmd) and HTML (docs/dataset.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