Last updated: 2024-02-06

Checks: 2 0

Knit directory: Cardiotoxicity/

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 3c04848. 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:    analysis/variance_values by gene.png
    Ignored:    data/41588_2018_171_MOESM3_ESMeQTL_ST2_for paper.csv
    Ignored:    data/Arr_GWAS.txt
    Ignored:    data/Arr_geneset.RDS
    Ignored:    data/BC_cell_lines.csv
    Ignored:    data/BurridgeDOXTOX.RDS
    Ignored:    data/CADGWASgene_table.csv
    Ignored:    data/CAD_geneset.RDS
    Ignored:    data/CALIMA_Data/
    Ignored:    data/CMD04_75DRCviability.csv
    Ignored:    data/CMD04_87DRCviability.csv
    Ignored:    data/CMD05_75DRCviability.csv
    Ignored:    data/CMD05_87DRCviability.csv
    Ignored:    data/Clamp_Summary.csv
    Ignored:    data/Cormotif_24_k1-5_raw.RDS
    Ignored:    data/Counts_RNA_ERMatthews.txt
    Ignored:    data/DAgostres24.RDS
    Ignored:    data/DAtable1.csv
    Ignored:    data/DDEMresp_list.csv
    Ignored:    data/DDE_reQTL.txt
    Ignored:    data/DDEresp_list.csv
    Ignored:    data/DEG-GO/
    Ignored:    data/DEG_cormotif.RDS
    Ignored:    data/DF_Plate_Peak.csv
    Ignored:    data/DRC48hoursdata.csv
    Ignored:    data/Da24counts.txt
    Ignored:    data/Dx24counts.txt
    Ignored:    data/Dx_reQTL_specific.txt
    Ignored:    data/EPIstorelist24.RDS
    Ignored:    data/Ep24counts.txt
    Ignored:    data/FC_necela.RDS
    Ignored:    data/FC_necela_names.RDS
    Ignored:    data/Full_LD_rep.csv
    Ignored:    data/GOIsig.csv
    Ignored:    data/GOplots.R
    Ignored:    data/GTEX_setsimple.csv
    Ignored:    data/GTEX_sig24.RDS
    Ignored:    data/GTEx_gene_list.csv
    Ignored:    data/HFGWASgene_table.csv
    Ignored:    data/HF_geneset.RDS
    Ignored:    data/Heart_Left_Ventricle.v8.egenes.txt
    Ignored:    data/Heatmap_mat.RDS
    Ignored:    data/Heatmap_sig.RDS
    Ignored:    data/Hf_GWAS.txt
    Ignored:    data/K_cluster
    Ignored:    data/K_cluster_kisthree.csv
    Ignored:    data/K_cluster_kistwo.csv
    Ignored:    data/Knowles_log2cpm_real.RDS
    Ignored:    data/Knowles_variation_data.RDS
    Ignored:    data/Knowles_variation_data_conc.RDS
    Ignored:    data/Knowlesvarlist.RDS
    Ignored:    data/LD50_05via.csv
    Ignored:    data/LDH48hoursdata.csv
    Ignored:    data/Mt24counts.txt
    Ignored:    data/NoRespDEG_final.csv
    Ignored:    data/RINsamplelist.txt
    Ignored:    data/RNA_seq_trial.RDS
    Ignored:    data/Schneider_GWAS.txt
    Ignored:    data/Seonane2019supp1.txt
    Ignored:    data/Sup_replicate_values.csv
    Ignored:    data/TMMnormed_x.RDS
    Ignored:    data/TOP2Bi-24hoursGO_analysis.csv
    Ignored:    data/TR24counts.txt
    Ignored:    data/TableS10.csv
    Ignored:    data/TableS11.csv
    Ignored:    data/TableS9.csv
    Ignored:    data/Top2_expression.RDS
    Ignored:    data/Top2biresp_cluster24h.csv
    Ignored:    data/Var_test_list.RDS
    Ignored:    data/Var_test_list24.RDS
    Ignored:    data/Var_test_list24alt.RDS
    Ignored:    data/Var_test_list3.RDS
    Ignored:    data/Vargenes.RDS
    Ignored:    data/Viabilitylistfull.csv
    Ignored:    data/allexpressedgenes.txt
    Ignored:    data/allfinal3hour.RDS
    Ignored:    data/allgenes.txt
    Ignored:    data/allmatrix.RDS
    Ignored:    data/allmymatrix.RDS
    Ignored:    data/annotation_data_frame.RDS
    Ignored:    data/averageviabilitytable.RDS
    Ignored:    data/averageviabilitytable.csv
    Ignored:    data/avgLD50.RDS
    Ignored:    data/avg_LD50.RDS
    Ignored:    data/avg_via_table.csv
    Ignored:    data/backGL.txt
    Ignored:    data/burr_genes.RDS
    Ignored:    data/calcium_data.RDS
    Ignored:    data/clamp_summary.RDS
    Ignored:    data/cormotif_3hk1-8.RDS
    Ignored:    data/cormotif_initalK5.RDS
    Ignored:    data/cormotif_initialK5.RDS
    Ignored:    data/cormotif_initialall.RDS
    Ignored:    data/cormotifprobs.csv
    Ignored:    data/counts24hours.RDS
    Ignored:    data/cpmcount.RDS
    Ignored:    data/cpmnorm_counts.csv
    Ignored:    data/crispr_genes.csv
    Ignored:    data/ctnnt_results.txt
    Ignored:    data/cvd_GWAS.txt
    Ignored:    data/dat_cpm.RDS
    Ignored:    data/data_outline.txt
    Ignored:    data/drug_noveh1.csv
    Ignored:    data/efit2.RDS
    Ignored:    data/efit2_final.RDS
    Ignored:    data/efit2results.RDS
    Ignored:    data/ensembl_backup.RDS
    Ignored:    data/ensgtotal.txt
    Ignored:    data/filcpm_counts.RDS
    Ignored:    data/filenameonly.txt
    Ignored:    data/filtered_cpm_counts.csv
    Ignored:    data/filtered_raw_counts.csv
    Ignored:    data/filtermatrix_x.RDS
    Ignored:    data/folder_05top/
    Ignored:    data/framefun24.RDS
    Ignored:    data/geneDoxonlyQTL.csv
    Ignored:    data/gene_corr_df.RDS
    Ignored:    data/gene_corr_frame.RDS
    Ignored:    data/gene_prob_tran3h.RDS
    Ignored:    data/gene_probabilityk5.RDS
    Ignored:    data/geneset_24.RDS
    Ignored:    data/gostresTop2bi_ER.RDS
    Ignored:    data/gostresTop2bi_LR
    Ignored:    data/gostresTop2bi_LR.RDS
    Ignored:    data/gostresTop2bi_TI.RDS
    Ignored:    data/gostrescoNR
    Ignored:    data/gtex/
    Ignored:    data/heartgenes.csv
    Ignored:    data/highly_var_genelist.RDS
    Ignored:    data/hsa_kegg_anno.RDS
    Ignored:    data/individualDRCfile.RDS
    Ignored:    data/individual_DRC48.RDS
    Ignored:    data/individual_LDH48.RDS
    Ignored:    data/indv_noveh1.csv
    Ignored:    data/kegglistDEG.RDS
    Ignored:    data/kegglistDEG24.RDS
    Ignored:    data/kegglistDEG3.RDS
    Ignored:    data/knowfig4.csv
    Ignored:    data/knowfig5.csv
    Ignored:    data/label_list.RDS
    Ignored:    data/ld50_table.csv
    Ignored:    data/mean_vardrug1.csv
    Ignored:    data/mean_varframe.csv
    Ignored:    data/mymatrix.RDS
    Ignored:    data/new_ld50avg.RDS
    Ignored:    data/nonresponse_cluster24h.csv
    Ignored:    data/norm_LDH.csv
    Ignored:    data/norm_counts.csv
    Ignored:    data/old_sets/
    Ignored:    data/organized_drugframe.csv
    Ignored:    data/pca_all_anno.csv
    Ignored:    data/plan2plot.png
    Ignored:    data/plot_intv_list.RDS
    Ignored:    data/plot_list_DRC.RDS
    Ignored:    data/qval24hr.RDS
    Ignored:    data/qval3hr.RDS
    Ignored:    data/qvalueEPItemp.RDS
    Ignored:    data/raw_counts.csv
    Ignored:    data/response_cluster24h.csv
    Ignored:    data/sampsettrz.RDS
    Ignored:    data/schneider_closest_output.RDS
    Ignored:    data/sigVDA24.txt
    Ignored:    data/sigVDA3.txt
    Ignored:    data/sigVDX24.txt
    Ignored:    data/sigVDX3.txt
    Ignored:    data/sigVEP24.txt
    Ignored:    data/sigVEP3.txt
    Ignored:    data/sigVMT24.txt
    Ignored:    data/sigVMT3.txt
    Ignored:    data/sigVTR24.txt
    Ignored:    data/sigVTR3.txt
    Ignored:    data/siglist.RDS
    Ignored:    data/siglist_final.RDS
    Ignored:    data/siglist_old.RDS
    Ignored:    data/slope_table.csv
    Ignored:    data/supp10_24hlist.RDS
    Ignored:    data/supp10_3hlist.RDS
    Ignored:    data/supp_normLDH48.RDS
    Ignored:    data/supp_pca_all_anno.RDS
    Ignored:    data/supp_viadata.csv
    Ignored:    data/table3a.omar
    Ignored:    data/test_run_sample_list.txt
    Ignored:    data/testlist.txt
    Ignored:    data/toplistall.RDS
    Ignored:    data/trtonly_24h_genes.RDS
    Ignored:    data/trtonly_3h_genes.RDS
    Ignored:    data/tvl24hour.txt
    Ignored:    data/tvl24hourw.txt
    Ignored:    data/venn_code.R
    Ignored:    data/viability.RDS

Untracked files:
    Untracked:  .RDataTmp
    Untracked:  .RDataTmp1
    Untracked:  .RDataTmp2
    Untracked:  .RDataTmp3
    Untracked:  3hr all.pdf
    Untracked:  Code_files_list.csv
    Untracked:  Data_files_list.csv
    Untracked:  Doxorubicin_vehicle_3_24.csv
    Untracked:  Doxtoplist.csv
    Untracked:  EPIqvalue_analysis.Rmd
    Untracked:  Final.sup.pdf
    Untracked:  GWAS_list_of_interest.xlsx
    Untracked:  KEGGpathwaylist.R
    Untracked:  NA
    Untracked:  OmicNavigator_learn.R
    Untracked:  SNP_egenes_allfiles.RDS
    Untracked:  SNP_frame_pdf
    Untracked:  SNP_frame_pdf.pdf
    Untracked:  SigDoxtoplist.csv
    Untracked:  analysis/DRC_viability_check.Rmd
    Untracked:  analysis/New_code_dec-23.R
    Untracked:  analysis/cellcycle_kegg_genes.R
    Untracked:  analysis/ciFIT.R
    Untracked:  analysis/export_to_excel.R
    Untracked:  analysis/featureCountsPLAY.R
    Untracked:  cleanupfiles_script.R
    Untracked:  code/biomart_gene_names.R
    Untracked:  code/constantcode.R
    Untracked:  code/corMotifcustom.R
    Untracked:  code/cpm_boxplot.R
    Untracked:  code/extracting_ggplot_data.R
    Untracked:  code/movingfilesto_ppl.R
    Untracked:  code/pearson_extract_func.R
    Untracked:  code/pearson_tox_extract.R
    Untracked:  code/plot1C.fun.R
    Untracked:  code/spearman_extract_func.R
    Untracked:  code/venndiagramcolor_control.R
    Untracked:  cormotif_p.post.list_4.csv
    Untracked:  figS1024h.pdf
    Untracked:  final.pdf
    Untracked:  individual-legenddark2.png
    Untracked:  installed_old.rda
    Untracked:  listoftranscripts
    Untracked:  motif_ER.txt
    Untracked:  motif_LR.txt
    Untracked:  motif_NR.txt
    Untracked:  motif_TI.txt
    Untracked:  output/ABHD8_dif_values.RDS
    Untracked:  output/C3orf18_dif_values.RDS
    Untracked:  output/Cardiotox_dif_values.RDS
    Untracked:  output/DNR_DEGlist.csv
    Untracked:  output/DNRvenn.RDS
    Untracked:  output/DOX_DEGlist.csv
    Untracked:  output/DOX_de_goi.csv
    Untracked:  output/DOXvenn.RDS
    Untracked:  output/EEF1B2_dif_values.RDS
    Untracked:  output/EEIG1_dif_values.RDS
    Untracked:  output/EPI_DEGlist.csv
    Untracked:  output/EPIvenn.RDS
    Untracked:  output/ESGN_rds.RDS
    Untracked:  output/FC_necela.RDS
    Untracked:  output/FC_necela_names.RDS
    Untracked:  output/FRS2_dif_values.RDS
    Untracked:  output/Figures/
    Untracked:  output/GTEXv8_gene_median_tpm.RDS
    Untracked:  output/GTEXv8_gene_tpm_heart_left_ventricle.RDS
    Untracked:  output/HDDC2_dif_values.RDS
    Untracked:  output/HER2_gene.RDS
    Untracked:  output/KEGGcellcyclegenes.RDS
    Untracked:  output/Knowles_S13.csv
    Untracked:  output/Knowles_log2cpm.csv
    Untracked:  output/Knowles_supp13.csv
    Untracked:  output/LD50tox_table.RDS
    Untracked:  output/MTX_DEGlist.csv
    Untracked:  output/MTXvenn.RDS
    Untracked:  output/PEX16_dif_values.RDS
    Untracked:  output/RASIP1_dif_values.RDS
    Untracked:  output/RMI1_dif_values.RDS
    Untracked:  output/RSID_QTL_list_full.txt
    Untracked:  output/SETA_analysis_reyes.RDS
    Untracked:  output/SGWAS_top50_order.csv
    Untracked:  output/SLC27A1_dif_values.RDS
    Untracked:  output/SLC28A3_dif_values.RDS
    Untracked:  output/SNP_egenes_allfiles.RDS
    Untracked:  output/SNP_list_ID.RDS
    Untracked:  output/SNP_list_full.txt
    Untracked:  output/SNP_supp.RDS
    Untracked:  output/TGFBR3L_dif_values.RDS
    Untracked:  output/TNS2_dif_values.RDS
    Untracked:  output/TOP_50SNPreffile.csv
    Untracked:  output/TRZ_DEGlist.csv
    Untracked:  output/TableS8.csv
    Untracked:  output/Volcanoplot_10
    Untracked:  output/Volcanoplot_10.RDS
    Untracked:  output/ZNF740_dif_values.RDS
    Untracked:  output/allfinal_sup10.RDS
    Untracked:  output/counts_v8_heart_left_ventricle_gct.RDS
    Untracked:  output/crisprfoldchange.RDS
    Untracked:  output/endocytosisgenes.csv
    Untracked:  output/expre7k.csv
    Untracked:  output/expressed_egenes_by_RSID.csv
    Untracked:  output/gene_corr_fig9.RDS
    Untracked:  output/genes.RDS
    Untracked:  output/legend_b.RDS
    Untracked:  output/motif_ERrep.RDS
    Untracked:  output/motif_LRrep.RDS
    Untracked:  output/motif_NRrep.RDS
    Untracked:  output/motif_TI_rep.RDS
    Untracked:  output/near_genes_SNP1.RDS
    Untracked:  output/necela_list_test.RDS
    Untracked:  output/necela_val_genes.RDS
    Untracked:  output/output-old/
    Untracked:  output/rank24genes.csv
    Untracked:  output/rank3genes.csv
    Untracked:  output/sequencinginformationforsupp.csv
    Untracked:  output/sequencinginformationforsupp.prn
    Untracked:  output/sigVDA24.txt
    Untracked:  output/sigVDA3.txt
    Untracked:  output/sigVDX24.txt
    Untracked:  output/sigVDX3.txt
    Untracked:  output/sigVEP24.txt
    Untracked:  output/sigVEP3.txt
    Untracked:  output/sigVMT24.txt
    Untracked:  output/sigVMT3.txt
    Untracked:  output/sigVTR24.txt
    Untracked:  output/sigVTR3.txt
    Untracked:  output/supplementary_motif_list_GO.RDS
    Untracked:  output/test_biomart_run.RDS
    Untracked:  output/toptablebydrug.RDS
    Untracked:  output/trop_knowles_fun.csv
    Untracked:  output/tvl24hour.txt
    Untracked:  output/x_counts.RDS
    Untracked:  reneebasecode.R

Unstaged changes:
    Modified:   analysis/DRC_analysis.Rmd
    Modified:   analysis/Figure4.Rmd
    Modified:   analysis/Figure5.Rmd
    Modified:   analysis/Figure6.Rmd
    Modified:   analysis/GTEx_genes.Rmd
    Deleted:    analysis/Knowles2019.Rmd
    Modified:   output/daplot.RDS
    Modified:   output/dxplot.RDS
    Modified:   output/epplot.RDS
    Modified:   output/mtplot.RDS
    Modified:   output/plan2plot.png
    Modified:   output/trplot.RDS
    Modified:   output/veplot.RDS

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/index.Rmd) and HTML (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
Rmd 3c04848 reneeisnowhere 2024-02-06 wflow_publish("analysis/index.Rmd")
html e36efad reneeisnowhere 2023-09-28 Build site.
Rmd 5e9df35 reneeisnowhere 2023-09-28 rearrange and add CSS and links
html 2e39a03 reneeisnowhere 2023-09-27 Build site.
html 2dc87dd reneeisnowhere 2023-09-27 Build site.
Rmd 37db1a6 reneeisnowhere 2023-09-27 wflow_publish("analysis/index.Rmd")
Rmd bf0aab0 reneeisnowhere 2023-09-27 first change after move
html d0f858e reneeisnowhere 2023-07-21 Build site.
Rmd 9faba14 reneeisnowhere 2023-07-21 adding Var Genes page
html e48b9f5 reneeisnowhere 2023-07-14 Build site.
Rmd fcc6805 reneeisnowhere 2023-07-14 adding link to variance scrip for Michelle
html 8a63b2e reneeisnowhere 2023-06-30 Build site.
Rmd eca1c8e reneeisnowhere 2023-06-30 update index
html 2cf8d34 reneeisnowhere 2023-06-23 Build site.
Rmd 2dcfd91 reneeisnowhere 2023-06-23 adding supp figure link
html 87453aa reneeisnowhere 2023-06-23 Build site.
Rmd 3cc507e reneeisnowhere 2023-06-23 updating plots
html 554ef92 reneeisnowhere 2023-06-23 Build site.
html f7e433b reneeisnowhere 2023-06-16 Build site.
Rmd 3d4ca64 reneeisnowhere 2023-06-16 updates on Friday
html bd0e45f reneeisnowhere 2023-06-15 Build site.
Rmd 1a1a034 reneeisnowhere 2023-06-15 updates galore
html 2923438 reneeisnowhere 2023-06-14 Build site.
Rmd f986dee reneeisnowhere 2023-06-14 update index
html 8b862b3 reneeisnowhere 2023-06-13 Build site.
Rmd 5ede159 reneeisnowhere 2023-06-13 finalized plots and curves for slope and LD50 and index updata
html 4b32b73 reneeisnowhere 2023-05-22 Build site.
Rmd fecbbaf reneeisnowhere 2023-05-22 update list
html 3f2250f reneeisnowhere 2023-05-17 Build site.
Rmd a9e025d reneeisnowhere 2023-05-17 spelling and format update
html d0eaef8 reneeisnowhere 2023-04-20 Build site.
Rmd 5e61428 reneeisnowhere 2023-04-20 updating calcium graphs and index
html 1639244 reneeisnowhere 2023-04-17 Build site.
Rmd d007af4 reneeisnowhere 2023-04-17 new links
html 7f62d67 reneeisnowhere 2023-04-17 Build site.
Rmd 363ddad reneeisnowhere 2023-04-17 update with GO links
html 9e37491 reneeisnowhere 2023-04-16 Build site.
Rmd 41bc19a reneeisnowhere 2023-04-16 updated Cormotif data
html b266b76 reneeisnowhere 2023-04-10 Build site.
Rmd d3f8cf7 reneeisnowhere 2023-04-10 update push of new data
html 84e723b reneeisnowhere 2023-02-10 Build site.
Rmd accc241 reneeisnowhere 2023-02-10 updates for the week
html f147cf9 reneeisnowhere 2023-02-01 Build site.
Rmd 90da9c1 reneeisnowhere 2023-01-31 update index
html 146a31a reneeisnowhere 2023-01-20 Build site.
Rmd b7eac76 reneeisnowhere 2023-01-20 updating GO
html 6c21cf8 reneeisnowhere 2023-01-20 Build site.
Rmd 443a9f3 reneeisnowhere 2023-01-20 adding in GO analysis
html 8107886 reneeisnowhere 2023-01-20 Build site.
html 0950d4f reneeisnowhere 2023-01-13 Build site.
Rmd f03a013 reneeisnowhere 2023-01-13 update the link
Rmd cfc3e81 reneeisnowhere 2023-01-13 updating readme and index
html 7eccdb8 reneeisnowhere 2023-01-12 Build site.
Rmd 93c4409 reneeisnowhere 2023-01-12 try again
Rmd ae8266e reneeisnowhere 2023-01-12 updating the rmarkdown
html df8a845 reneeisnowhere 2023-01-11 Build site.
Rmd 98fe131 reneeisnowhere 2023-01-11 wflow_publish(c("analysis/license.Rmd", "analysis/index.Rmd"))
Rmd be977ac reneeisnowhere 2023-01-10 testing interface
Rmd 48a3f62 reneeisnowhere 2023-01-10 attempting again
html 7c3d440 reneeisnowhere 2023-01-10 Build site.
html 0d9d258 reneeisnowhere 2023-01-09 Build site.
Rmd 3aa4631 reneeisnowhere 2023-01-09 Trial updates
html 9e0f8ee reneeisnowhere 2023-01-09 Build site.
Rmd 3b61ad1 reneeisnowhere 2023-01-09 Start workflowr project.

Welcome to my workflowr Cardiotoxicity research website. I am using workflowr to create reproducible code and data analysis.

Full data set information

Bayesian gene analysis

Bayesian gene analysis