Last updated: 2026-01-06

Checks: 1 1

Knit directory: DXR_website/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Repository version: c3ccfea

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version c3ccfea. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    DXR_website/data/
    Ignored:    code/Flow_Purity_Stressor_Boxplots_EMP_250226.R
    Ignored:    data/CDKN1A_geneplot_Dox.RDS
    Ignored:    data/Cormotif_dox.RDS
    Ignored:    data/Cormotif_prob_gene_list.RDS
    Ignored:    data/Cormotif_prob_gene_list_doxonly.RDS
    Ignored:    data/Counts_RNA_EMPfortmiller.txt
    Ignored:    data/DMSO_TNN13_plot.RDS
    Ignored:    data/DOX_TNN13_plot.RDS
    Ignored:    data/DOXgeneplots.RDS
    Ignored:    data/ExpressionMatrix_EMP.csv
    Ignored:    data/Ind1_DOX_Spearman_plot.RDS
    Ignored:    data/Ind6REP_Spearman_list.csv
    Ignored:    data/Ind6REP_Spearman_plot.RDS
    Ignored:    data/Ind6REP_Spearman_set.csv
    Ignored:    data/Ind6_Spearman_plot.RDS
    Ignored:    data/MDM2_geneplot_Dox.RDS
    Ignored:    data/Master_summary_75-1_EMP_250811_final.csv
    Ignored:    data/Master_summary_87-1_EMP_250811_final.csv
    Ignored:    data/Metadata.csv
    Ignored:    data/Metadata_2_norep_update.RDS
    Ignored:    data/Metadata_update.csv
    Ignored:    data/QC/
    Ignored:    data/Recovery_flow_purity.csv
    Ignored:    data/SIRT1_geneplot_Dox.RDS
    Ignored:    data/Sample_annotated.csv
    Ignored:    data/SpearmanHeatmapMatrix_EMP
    Ignored:    data/VolcanoPlot_D144R_original_EMP_250623.png
    Ignored:    data/VolcanoPlot_D24R_original_EMP_250623.png
    Ignored:    data/VolcanoPlot_D24T_original_EMP_250623.png
    Ignored:    data/annot_dox.RDS
    Ignored:    data/annot_list_hm.csv
    Ignored:    data/cormotif_dxr_1.RDS
    Ignored:    data/cormotif_dxr_2.RDS
    Ignored:    data/counts/
    Ignored:    data/counts_DE_df_dox.RDS
    Ignored:    data/counts_DE_raw_data.RDS
    Ignored:    data/counts_raw_filt.RDS
    Ignored:    data/counts_raw_matrix.RDS
    Ignored:    data/counts_raw_matrix_EMP_250514.csv
    Ignored:    data/d24_Spearman_plot.RDS
    Ignored:    data/dge_calc_dxr.RDS
    Ignored:    data/dge_calc_matrix.RDS
    Ignored:    data/ensembl_backup_dox.RDS
    Ignored:    data/fC_AllCounts.RDS
    Ignored:    data/fC_DOXCounts.RDS
    Ignored:    data/featureCounts_Concat_Matrix_DOXSamples_EMP_250430.csv
    Ignored:    data/featureCounts_DOXdata_updatedind.RDS
    Ignored:    data/filcpm_colnames_matrix.csv
    Ignored:    data/filcpm_matrix.csv
    Ignored:    data/filt_gene_list_dox.RDS
    Ignored:    data/filter_gene_list_final.RDS
    Ignored:    data/final_data/
    Ignored:    data/gene_clustlike_motif.RDS
    Ignored:    data/gene_postprob_motif.RDS
    Ignored:    data/genedf_dxr.RDS
    Ignored:    data/genematrix_dox.RDS
    Ignored:    data/genematrix_dxr.RDS
    Ignored:    data/heartgenes.csv
    Ignored:    data/heartgenes_dox.csv
    Ignored:    data/image_intensity_stats_all_conditions.csv
    Ignored:    data/image_level_stats_all_conditions.csv
    Ignored:    data/image_level_summary_yH2AX_quant.csv
    Ignored:    data/ind_num_dox.RDS
    Ignored:    data/ind_num_dxr.RDS
    Ignored:    data/initial_cormotif.RDS
    Ignored:    data/initial_cormotif_dox.RDS
    Ignored:    data/low_nuclei_samples.csv
    Ignored:    data/low_veh_samples.csv
    Ignored:    data/new/
    Ignored:    data/new_cormotif_dox.RDS
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    Ignored:    data/plot_leg_d.RDS
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    Ignored:    data/plot_theme_custom.RDS
    Ignored:    data/process_gene_data_funct.RDS
    Ignored:    data/raw_mean_all_10X.png
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    Ignored:    data/ruv/
    Ignored:    data/summary_all_IF_ROI.RDS
    Ignored:    data/tableED_GOBP.RDS
    Ignored:    data/tableESR_GOBP_postprob.RDS
    Ignored:    data/tableLD_GOBP.RDS
    Ignored:    data/tableLR_GOBP_postprob.RDS
    Ignored:    data/tableNR_GOBP.RDS
    Ignored:    data/tableNR_GOBP_postprob.RDS
    Ignored:    data/table_incsus_genes_GOBP_RUV.RDS
    Ignored:    data/table_motif1_GOBP_d.RDS
    Ignored:    data/table_motif1_genes_GOBP.RDS
    Ignored:    data/table_motif2_GOBP_d.RDS
    Ignored:    data/table_motif3_genes_GOBP.RDS
    Ignored:    data/thing.R
    Ignored:    data/top.table_V.D144r_dox.RDS
    Ignored:    data/top.table_V.D24_dox.RDS
    Ignored:    data/top.table_V.D24r_dox.RDS
    Ignored:    data/yH2AX_75-1_EMP_250811.csv
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    Ignored:    data/yH2AX_Boxplots_MeanIntensity_10X_EMP_250811.png
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    Ignored:    data/yH2AX_Boxplots_MeanIntensity_20X_NormtoMax_EMP_250811.png
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    Ignored:    data/yH2AX_Boxplots_MedianIntensity_NormtoMax_EMP_250811.png
    Ignored:    data/yH2AX_Boxplots_Quant_10X_EMP_250817.png
    Ignored:    data/yH2AX_Boxplots_Quant_20X_EMP_250817.png
    Ignored:    data/yh2ax_all_df_EMP_250812.csv

Unstaged changes:
    Modified:   DXR_website/analysis/index.Rmd

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 (DXR_website/analysis/index.Rmd) and HTML (DXR_website/docs/index.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 c3ccfea emmapfort 2026-01-06 Build site.
html c382b38 emmapfort 2026-01-06 Build site.
Rmd cd535e9 emmapfort 2026-01-06 Final Website Touches 01/06/25 EMP
html 7f22593 emmapfort 2026-01-05 Build site.
html 5b0f715 emmapfort 2025-12-09 Build site.
html f088a00 emmapfort 2025-12-09 website updates
Rmd a967d53 emmapfort 2025-12-09 Update website and analysis chunks
html c523397 emmapfort 2025-12-01 Build site.
html 0f7b54c emmapfort 2025-12-01 Build site.
Rmd 099ed2b emmapfort 2025-12-01 New Website Commit
Rmd 9a22c3c emmapfort 2025-12-01 Updated Analysis 12/01/25

Welcome!

This website contains the analysis leading up to and behind each figure. Click below to view my code and see my workflow. Main figures and supplementary figures are ordered chronologically with each piece labelled in the table of contents.

Flow Cytometry, Dose-response, yH2AX IF