Last updated: 2023-04-10
Checks: 2 0
Knit directory: Cardiotoxicity/
This reproducible R Markdown analysis was created with workflowr (version 1.7.0). 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 d3f8cf7. 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: data/ACresponse_cluster24h.csv
Ignored: data/Clamp_Summary.csv
Ignored: data/Cormotif_24_k1-5_raw.RDS
Ignored: data/DAtable1.csv
Ignored: data/DDE_reQTL.txt
Ignored: data/DDEresp_list.csv
Ignored: data/DEG_cormotif.RDS
Ignored: data/DF_Plate_Peak.csv
Ignored: data/Da24counts.txt
Ignored: data/Dx24counts.txt
Ignored: data/Dx_reQTL_specific.txt
Ignored: data/Ep24counts.txt
Ignored: data/GOplots.R
Ignored: data/K_cluster
Ignored: data/K_cluster_kisthree.csv
Ignored: data/K_cluster_kistwo.csv
Ignored: data/Mt24counts.txt
Ignored: data/RINsamplelist.txt
Ignored: data/Seonane2019supp1.txt
Ignored: data/TOP2Bi-24hoursGO_analysis.csv
Ignored: data/TR24counts.txt
Ignored: data/Top2biresp_cluster24h.csv
Ignored: data/Viabilitylistfull.csv
Ignored: data/allexpressedgenes.txt
Ignored: data/allgenes.txt
Ignored: data/allmatrix.RDS
Ignored: data/avgLD50.RDS
Ignored: data/backGL.txt
Ignored: data/cormotif_3hk1-8.RDS
Ignored: data/cormotif_ER_respint.txt
Ignored: data/cormotif_ER_respset.txt
Ignored: data/cormotif_LR_respint.txt
Ignored: data/cormotif_LR_respset.txt
Ignored: data/cormotif_NRset.txt
Ignored: data/cormotif_TI_respint.txt
Ignored: data/cormotif_TI_respset.txt
Ignored: data/cormotif_initalK5.RDS
Ignored: data/cormotif_initialK5.RDS
Ignored: data/counts24hours.RDS
Ignored: data/cpmnorm_counts.csv
Ignored: data/dat_cpm.RDS
Ignored: data/data_outline.txt
Ignored: data/efit2results.RDS
Ignored: data/ensgtotal.txt
Ignored: data/filenameonly.txt
Ignored: data/filtered_cpm_counts.csv
Ignored: data/filtermatrix_x.RDS
Ignored: data/folder_05top/
Ignored: data/gene_prob_tran3h.RDS
Ignored: data/gene_probabilityk5.RDS
Ignored: data/individualDRCfile.RDS
Ignored: data/knowles56.GMT
Ignored: data/knowlesGMT.GMT
Ignored: data/mymatrix.RDS
Ignored: data/nonresponse_cluster24h.csv
Ignored: data/norm_LDH.csv
Ignored: data/norm_counts.csv
Ignored: data/plan2plot.png
Ignored: data/raw_counts.csv
Ignored: data/response_cluster24h.csv
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/table3a.omar
Ignored: data/tvl24hour.txt
Ignored: data/tvl24hourw.txt
Ignored: data/venn_code.R
Untracked files:
Untracked: .RDataTmp
Untracked: .RDataTmp1
Untracked: code/extra_code.R
Untracked: output/output-old/
Untracked: reneebasecode.R
Unstaged changes:
Modified: analysis/DRC_analysis.Rmd
Modified: code/eQTLcodes.R
Deleted: output/Cormotif.svg
Deleted: output/Ctrxn24-3-23.svg
Deleted: output/Ctxnrate3-23.png
Deleted: output/Decay_Slope3-23.svg
Deleted: output/ERmotif5_LFC.svg
Deleted: output/GOBP_motif345.svg
Deleted: output/KEGGmotif_345.svg
Deleted: output/LD503-21-23.png
Deleted: output/LDH_24-3-23.svg
Deleted: output/LDH_243-23.svg
Deleted: output/LFCbytreatment3-25.svg
Deleted: output/LFCmotif4_LR.svg
Deleted: output/LR_RespMoti4.svg
Deleted: output/MeanAmp243-23.svg
Deleted: output/NRmotif1_LFC.svg
Deleted: output/Rise_Slope3-23.svg
Deleted: output/TI_LFC.svg
Deleted: output/TVLcorr3-23.svg
Deleted: output/TropI3-23.svg
Deleted: output/Venn24DEG-3-24.png
Deleted: output/motif1NR_LFC.svg
Deleted: output/motif3TIlfc3-25.svg
Deleted: output/motif4LR3-25LFC.svg
Deleted: output/motif5ER-LFC-3-25.svg
Deleted: output/nolegendLDH.svg
Deleted: output/resultsigVDA24.csv
Deleted: output/tropI_24-3-23.svg
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 | 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 research website. I am using workflowr to create reproducible code and data analysis.
Click on this link to see my results from the full run!!!
Click on this link to see my results from the first analysis
You can also look at my page of GO analysis. This page will eventually contain all my Gene Enrichment analysis. [GSEA analysis]https://reneeisnowhere.github.io/Cardiotoxicity/GO_analysis.html [LDH analysis]https://reneeisnowhere.github.io/Cardiotoxicity/LDH_analysis.html