Last updated: 2024-03-21

Checks: 2 0

Knit directory: mi_spatialomics/

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R Markdown file: up-to-date

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Repository version: e6213a5

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/deprecated/.DS_Store
    Ignored:    analysis/molecular_cartography_python/.DS_Store
    Ignored:    analysis/seqIF_python/.DS_Store
    Ignored:    analysis/seqIF_python/pixie/.DS_Store
    Ignored:    analysis/seqIF_python/pixie/cell_clustering/
    Ignored:    annotations/.DS_Store
    Ignored:    annotations/SeqIF/.DS_Store
    Ignored:    annotations/molkart/.DS_Store
    Ignored:    annotations/molkart/Figure1_regions/.DS_Store
    Ignored:    annotations/molkart/Supplementary_Figure4_regions/.DS_Store
    Ignored:    data/.DS_Store
    Ignored:    data/140623.calcagno_et_al.seurat_object.rds
    Ignored:    data/Calcagno2022_int_logNorm_annot.h5Seurat
    Ignored:    data/IC_03_IF_CCR2_CD68 cell numbers.xlsx
    Ignored:    data/Traditional_IF_absolute_cell_counts.csv
    Ignored:    data/Traditional_IF_relative_cell_counts.csv
    Ignored:    data/pixie.cell_table_size_normalized_cell_labels.csv
    Ignored:    data/results_cts_100.sqm
    Ignored:    data/seqIF_regions_annotations/
    Ignored:    data/seurat/
    Ignored:    output/.DS_Store
    Ignored:    output/mol_cart.harmony_object.h5Seurat
    Ignored:    output/molkart/
    Ignored:    output/proteomics/
    Ignored:    output/results_cts.lowres.125.sqm
    Ignored:    output/seqIF/
    Ignored:    pipeline_configs/.DS_Store
    Ignored:    plots/
    Ignored:    references/.DS_Store
    Ignored:    renv/.DS_Store
    Ignored:    renv/library/
    Ignored:    renv/staging/

Untracked files:
    Untracked:  analysis/deprecated/figures.supplementary_figureX.Rmd
    Untracked:  analysis/deprecated/figures.supplementary_figure_X.MistyR.Rmd

Unstaged changes:
    Deleted:    analysis/figures.supplementary_figureX.Rmd
    Deleted:    analysis/figures.supplementary_figure_X.MistyR.Rmd
    Deleted:    analysis/figures.supplementary_figure_X.proteomics_qc.Rmd
    Deleted:    figures/Figure_5.eps
    Deleted:    figures/Figure_5.pdf
    Deleted:    figures/Figure_5.png
    Deleted:    figures/Figure_5.svg
    Deleted:    figures/Supplementary_Figure_1_Molecular_Cartography_ROIs.png
    Deleted:    figures/Supplementary_figure_5.segmentation_metrics.poster.eps
    Modified:   figures/Supplementary_figure_X.proteomics.eps
    Modified:   figures/Supplementary_figure_X.proteomics.png
    Deleted:    results_cts.lowres.125.sqm

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/figures.Rmd) and HTML (docs/figures.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
Rmd 82f107f FloWuenne 2024-01-21 Updates to Molkart analysis.
Rmd f4d5c82 FloWuenne 2024-01-15 Latest update to Seurat analysis with reprocessed data.
html 2dcd178 FloWuenne 2023-12-06 wflow_publish("*")
Rmd 5dee03d FloWuenne 2023-09-04 Latest code update.
html 5dee03d FloWuenne 2023-09-04 Latest code update.
html d7ea71e FloWuenne 2023-08-11 Build site.
Rmd 64318a3 FloWuenne 2023-08-11 wflow_publish(c("analysis/molkart.process_quantifications_seurat.Rmd",
html 67e546d FloWuenne 2023-07-23 Build site.
html 59f6eae FloWuenne 2023-06-13 Build site.
Rmd e5d5982 FloWuenne 2023-06-13 Update Figure list.
html 5816aca FloWuenne 2023-06-12 Build site.
Rmd 3b5ca40 FloWuenne 2023-06-12 Added code for supplementary Figures.
html 3b5ca40 FloWuenne 2023-06-12 Added code for supplementary Figures.