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Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/obsolete/
    Ignored:    data/C133_Neeland_batch1/
    Ignored:    data/C133_Neeland_merged/
    Ignored:    output/dge_analysis/obsolete/
    Ignored:    renv/library/
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Untracked files:
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    Untracked:  analysis/13.0_DGE_analysis_macrophages_CF-vs-control-samples.Rmd
    Untracked:  analysis/13.3_DGE_analysis_macro-CCL.Rmd
    Untracked:  analysis/13.4_DGE_analysis_macro-IFI27.Rmd
    Untracked:  analysis/13.5_DGE_analysis_macro-lipid.Rmd
    Untracked:  analysis/13.6_DGE_analysis_macro-monocyte-derived.Rmd
    Untracked:  analysis/13.7_DGE_analysis_macro-proliferating.Rmd
    Untracked:  analysis/17.0_Figure_3.Rmd
    Untracked:  code/background_job.R
    Untracked:  code/reverse_modifier_severity_comparisons.sh
    Untracked:  data/Proteins_T-NK_07.10.24.csv
    Untracked:  data/Proteins_macs_07.10.24.csv
    Untracked:  data/cluster_annotations/marker_genes_TNK_figure_2.xlsx
    Untracked:  data/cluster_annotations/marker_genes_macrophages_figure_2.xlsx
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    Untracked:  data/cluster_annotations/marker_proteins_TNK_supp.xlsx
    Untracked:  data/cluster_annotations/marker_proteins_macrophages_supp.xlsx
    Untracked:  data/cluster_annotations/marker_proteins_other_supp.xlsx
    Untracked:  data/intermediate_objects/
    Untracked:  data/main_marker_genes.xlsx
    Untracked:  data/main_proteins.xlsx
    Untracked:  data/marker_genes_fig_2.xlsx

Unstaged changes:
    Modified:   .gitignore
    Modified:   analysis/09.0_integrate_cluster_macro_cells.Rmd
    Modified:   analysis/14.0_proportions_analysis_ann_level_1.Rmd
    Modified:   analysis/15.0_Figure_1.Rmd
    Modified:   analysis/16.0_Figure_2.Rmd
    Modified:   code/utility.R

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