Last updated: 2025-07-03
Checks: 2 0
Knit directory: CX5461_Project/
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.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
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 eca9f05. 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: .RData
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: 0.1 box.svg
Ignored: Rplot04.svg
Untracked files:
Untracked: 0.1 density.svg
Untracked: 0.1.emf
Untracked: 0.1.svg
Untracked: 0.5 box.svg
Untracked: 0.5 density.svg
Untracked: 0.5.svg
Untracked: Additional/
Untracked: Autosome factors.svg
Untracked: CX_5461_Pattern_Genes_24hr.csv
Untracked: CX_5461_Pattern_Genes_3hr.csv
Untracked: Cell viability box plot.svg
Untracked: DEG GO terms.svg
Untracked: DNA damage associated GO terms.svg
Untracked: DRC1.svg
Untracked: Figure 1.jpeg
Untracked: Figure 1.pdf
Untracked: Figure_CM_Purity.pdf
Untracked: G Quadruplex DEGs.svg
Untracked: PC2 Vs PC3 Autosome.svg
Untracked: PCA autosome.svg
Untracked: Rplot 18.svg
Untracked: Rplot.svg
Untracked: Rplot01.svg
Untracked: Rplot02.svg
Untracked: Rplot03.svg
Untracked: Rplot05.svg
Untracked: Rplot06.svg
Untracked: Rplot07.svg
Untracked: Rplot08.jpeg
Untracked: Rplot08.svg
Untracked: Rplot09.svg
Untracked: Rplot10.svg
Untracked: Rplot11.svg
Untracked: Rplot12.svg
Untracked: Rplot13.svg
Untracked: Rplot14.svg
Untracked: Rplot15.svg
Untracked: Rplot16.svg
Untracked: Rplot17.svg
Untracked: Rplot18.svg
Untracked: Rplot19.svg
Untracked: Rplot20.svg
Untracked: Rplot21.svg
Untracked: Rplot22.svg
Untracked: Rplot23.svg
Untracked: Rplot24.svg
Untracked: S15.pdf
Untracked: TOP2B.bed
Untracked: TS HPA (Violin).svg
Untracked: TS HPA.svg
Untracked: TS_HA.svg
Untracked: TS_HV.svg
Untracked: Violin HA.svg
Untracked: Violin HV (CX vs DOX).svg
Untracked: Violin HV.svg
Untracked: data/AF.csv
Untracked: data/AF_Mapped.csv
Untracked: data/AF_genes.csv
Untracked: data/Annotated_DOX_Gene_Table.csv
Untracked: data/BP/
Untracked: data/CAD_genes.csv
Untracked: data/Cardiotox.csv
Untracked: data/Cardiotox_mapped.csv
Untracked: data/Col_DEG_proportion_data.csv
Untracked: data/Col_DEGs.csv
Untracked: data/Corrmotif_GO/
Untracked: data/DOX_Vald.csv
Untracked: data/DOX_Vald_Mapped.csv
Untracked: data/DOX_alt.csv
Untracked: data/Entrez_Cardiotox.csv
Untracked: data/Entrez_Cardiotox_Mapped.csv
Untracked: data/GWAS.xlsx
Untracked: data/GWAS_SNPs.bed
Untracked: data/HF.csv
Untracked: data/HF_Mapped.csv
Untracked: data/HF_genes.csv
Untracked: data/Hypertension_genes.csv
Untracked: data/MI_genes.csv
Untracked: data/P53_Target_mapped.csv
Untracked: data/Sample_annotated.csv
Untracked: data/Samples.csv
Untracked: data/Samples.xlsx
Untracked: data/TOP2A.bed
Untracked: data/TOP2A_target.csv
Untracked: data/TOP2A_target_lit.csv
Untracked: data/TOP2A_target_lit_mapped.csv
Untracked: data/TOP2A_target_mapped.csv
Untracked: data/TOP2B.bed
Untracked: data/TOP2B_target.csv
Untracked: data/TOP2B_target_heatmap.csv
Untracked: data/TOP2B_target_heatmap_mapped.csv
Untracked: data/TOP2B_target_mapped.csv
Untracked: data/TS.csv
Untracked: data/TS_HPA.csv
Untracked: data/TS_HPA_mapped.csv
Untracked: data/Toptable_CX_0.1_24.csv
Untracked: data/Toptable_CX_0.1_3.csv
Untracked: data/Toptable_CX_0.1_48.csv
Untracked: data/Toptable_CX_0.5_24.csv
Untracked: data/Toptable_CX_0.5_3.csv
Untracked: data/Toptable_CX_0.5_48.csv
Untracked: data/Toptable_DOX_0.1_24.csv
Untracked: data/Toptable_DOX_0.1_3.csv
Untracked: data/Toptable_DOX_0.1_48.csv
Untracked: data/Toptable_DOX_0.5_24.csv
Untracked: data/Toptable_DOX_0.5_3.csv
Untracked: data/Toptable_DOX_0.5_48.csv
Untracked: data/count.tsv
Untracked: data/heatmap.csv
Untracked: data/ts_data_mapped
Untracked: results/
Untracked: run_bedtools.bat
Unstaged changes:
Deleted: analysis/Actox.Rmd
Modified: data/DEGs/Toptable_DOX_0.5_3.csv
Modified: data/DOX_0.5_48 (Combined).csv
Modified: data/Total_number_of_Mapped_reads_by_Individuals.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/about.Rmd) and HTML
(docs/about.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 | 3e72e52 | sayanpaul01 | 2025-01-29 | Added all missing docs files including total_reads_by_sample.html |
| Rmd | 3de5b6b | sayanpaul01 | 2025-01-29 | Start workflowr project. |
Describe your project.