Last updated: 2023-07-02

Checks: 1 1

Knit directory: mi_spatialomics/

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Repository version: 430aac1

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    data/.DS_Store
    Ignored:    data/.Rapp.history
    Ignored:    data/140623.calcagno_et_al.seurat_object.rds
    Ignored:    renv/.DS_Store
    Ignored:    renv/library/
    Ignored:    renv/staging/

Untracked files:
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    Untracked:  analysis/figures.supplementary_figure_X.proteomics_qc.Rmd
    Untracked:  code/functions.R
    Untracked:  figures/Figure_5.eps
    Untracked:  figures/Figure_5.pdf
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    Untracked:  figures/Supplementary_figure_X.proteomics.eps
    Untracked:  figures/Supplementary_figure_X.proteomics.png
    Untracked:  omnipathr-log/
    Untracked:  output/limma.full_statistics.tsv
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    Untracked:  output/proteomics.pathway_results.MIiz_MIremote.tsv
    Untracked:  output/proteomics.pca_res.rds
    Untracked:  output/proteomics.protein_missing_stats.tsv
    Untracked:  output/proteomics.snRNAseq_comp.tsv
    Untracked:  output/proteomics.vsn_norm_proteins.tsv
    Untracked:  references/

Unstaged changes:
    Modified:   analysis/data_analysis.Rmd
    Modified:   analysis/figures.supplementary_Figure_3.Rmd
    Modified:   analysis/proteomics.bulk_de_analysis.Rmd
    Modified:   analysis/proteomics.filter_proteomic_data.Rmd
    Modified:   analysis/proteomics.pathway_enrichment_analysis.Rmd
    Modified:   analysis/proteomics.scRNAseq_comparison.Rmd
    Deleted:    code/params_R.R
    Modified:   figures/Supplementary_figure_3.eps
    Modified:   figures/Supplementary_figure_3.png
    Modified:   output/mi_iz_specific_proteins.tsv
    Modified:   renv.lock

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Rmd 236130c FloWuenne 2023-06-20 Updating proteomic analysis.
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Rmd 2d015dd FloWuenne 2023-06-14 Finalized imputation with RF.
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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.
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Rmd 412d64f FloWuenne 2023-06-12 Fixed links in data_analysis
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Rmd ff0c849 FloWuenne 2023-06-12 wflow_publish("*")
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Rmd ebb85a5 FloWuenne 2023-06-12 Updated organization for proteomics data analysis.
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Rmd 62020bf FloWuenne 2023-06-12 Configure site header.

Molecular Cartography

  1. QC RNA spots