Files in GranderLab/miR34a_asRNA_project
The miR34AasRNAproject package facilitates the transparency and reproducibility of the miR34a asRNA project and associated publication.
.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
Dockerfile
NAMESPACE
R/QpcrFuns.R
R/data.R
R/gatherFigures.R
R/plotting.R
R/processFigures.R
R/survival.R
R/utils.R
README.md
data-raw/coding_potential_geiger.txt
data-raw/figure1c.txt
data-raw/figure1f.txt
data-raw/figure2a.txt
data-raw/figure2b.txt
data-raw/figure2c.txt
data-raw/figure2d.txt
data-raw/figure2e.txt
data-raw/figure3a.txt
data-raw/figure3b.txt
data-raw/figure3c.txt
data-raw/figure3d.txt
data-raw/figure4a.txt
data-raw/saveRDS.R
data-raw/supp_figure1a.txt
data-raw/supp_figure2e.txt
data-raw/supp_figure3c.txt
data-raw/supp_figure4a.txt
data-raw/supp_figure4c.txt
data-raw/supp_figure4d.txt
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_fb1t1_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_fb1t2_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_fb2t1_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_fb2t2_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_fb3t1_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_fb3t2_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_mb1t1_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_mb1t2_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_mb2t1_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_mb2t2_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_mb3t1_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_mb3t2_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_unstained-F4_Data Source - 1.csv
data-raw/supp_figure5b/day0/user1_Experiment 2018-04-08 094853_day0_unstained-mock_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_F4 0.1 b1_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_F4 0.1 b2_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_F4 0.1 b3_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_F4 HBSS b1_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_F4 HBSS b2_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_F4 HBSS b3_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_F4 normal b1_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_F4 normal b2_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_F4 normal b3_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_mock 0.1 b1_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_mock 0.1 b2_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_mock 0.1 b3_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_mock HBSS b1_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_mock HBSS b2_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_mock HBSS b3_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_mock normal b1_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_mock normal b2_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_mock normal b3_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_unstained F4 0.1_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_unstained F4 HBSS_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_unstained F4 normal_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_unstained mock 0.1_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_unstained mock HBSS_Data Source - 1.csv
data-raw/supp_figure5b/day1/user1_180509 Jason day1_day1_unstained mock normal_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 0.1 b1_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 0.1 b2_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 0.1 b3_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 HBSS b1_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 HBSS b2_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 HBSS b3_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 normal b1_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 normal b2_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 normal b3_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 unstained 0.1_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 unstained HBSS_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_F4 unstained normal_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock 0.1 b1_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock 0.1 b2_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock 0.1 b3_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock HBSS b1_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock HBSS b2_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock HBSS b3_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock normal b1_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock normal b2_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock normal b3_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock unstained 0.1_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock unstained HBSS_Data Source - 1.csv
data-raw/supp_figure5b/day2/user1_180510 Jason day2_day2_mock unstained normal_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 0.1 b1_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 0.1 b2_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 0.1 b3_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 HBSS b1_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 HBSS b2_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 HBSS b3_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 normal b1_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 normal b2_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 normal b3_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 unstained 0.1_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 unstained HBSS_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_F4 unstained normal_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock 0.1 b1_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock 0.1 b2_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock 0.1 b3_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock HBSS b1_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock HBSS b2_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock HBSS b3_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock normal b1_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock normal b2_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock normal b3_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock unstained 0.1_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock unstained HBSS_Data Source - 1.csv
data-raw/supp_figure5b/day3/user1_180511 Jason day3_day3_mock unstained normal_Data Source - 1.csv
data-raw/supp_figure7.txt
data-raw/supp_figure8.txt
data/coding_potential_geiger.rds
data/figure1c.rds
data/figure1f.rds
data/figure2a.rds
data/figure2b.rds
data/figure2c.rds
data/figure2d.rds
data/figure2e.rds
data/figure3a.rds
data/figure3b.rds
data/figure3c.rds
data/figure3d.rds
data/figure4a.rds
data/supp_figure1a.rds
data/supp_figure2d.rds
data/supp_figure2e.rds
data/supp_figure3c.rds
data/supp_figure4a.rds
data/supp_figure4c.rds
data/supp_figure4d.rds
data/supp_figure5b.rds
data/supp_figure7.rds
data/supp_figure8.rds
inst/coding_potential_geiger/coding_potential_geiger.Rmd
inst/docker/Dockerfile
inst/docker/dummy.Rmd
inst/docker/liftr.yml
inst/figure1a/figure1a.Rmd
inst/figure1a/figure1a.png
inst/figure1b/figure1b.Rmd
inst/figure1b/figure1b.png
inst/figure1c/figure1c.Rmd
inst/figure1c/figure1c.png
inst/figure1d/figure1d.Rmd
inst/figure1d/figure1d.png
inst/figure1e/figure1e.Rmd
inst/figure1e/figure1e.ai
inst/figure1e/figure1e.png
inst/figure1f/figure1f.Rmd
inst/figure1f/figure1f.png
inst/figure2a/figure2a.Rmd
inst/figure2a/figure2a.png
inst/figure2b/figure2b.Rmd
inst/figure2b/figure2b.png
inst/figure2c/figure2c.Rmd
inst/figure2c/figure2c.png
inst/figure2d/figure2d.Rmd
inst/figure2d/figure2d.pdf
inst/figure2e/figure2e.Rmd
inst/figure2e/figure2e.png
inst/figure3a/figure3a.Rmd
inst/figure3a/figure3a.png
inst/figure3b/figure3b.Rmd
inst/figure3b/figure3b.png
inst/figure3c/figure3c.Rmd
inst/figure3c/figure3c.pdf
inst/figure3c/figure3c.png
inst/figure3d/figure3d.Rmd
inst/figure3d/figure3d.png
inst/figure4a/figure4a.Rmd
inst/figure4a/figure4a.png
inst/figure4b/figure4b.Rmd
inst/figure4b/figure4b.png
inst/figure5/figure5.Rmd
inst/figure5/figure5.png
inst/manuscript/CDD/revision/An antisense RNA capable of modulating the expression of the tumor suppressor microRNA-formated_references-CDD.docx
inst/manuscript/CDD/revision/An antisense RNA capable of modulating the expression of the tumor suppressor microRNA.docx
inst/manuscript/CDD/revision/Figures/Figure1.ai
inst/manuscript/CDD/revision/Figures/Figure1.png
inst/manuscript/CDD/revision/Figures/Figure2.ai
inst/manuscript/CDD/revision/Figures/Figure2.png
inst/manuscript/CDD/revision/Figures/Figure3.ai
inst/manuscript/CDD/revision/Figures/Figure3.png
inst/manuscript/CDD/revision/Figures/Figure4.ai
inst/manuscript/CDD/revision/Figures/Figure4.png
inst/manuscript/CDD/revision/Figures/Figure5.png
inst/manuscript/CDD/revision/Letter to Editor.docx
inst/manuscript/CDD/revision/ORCIDs.txt
inst/manuscript/CDD/revision/Response to referees.md
inst/manuscript/CDD/revision/Response to referees.pdf
inst/manuscript/CDD/revision/Supplementary_Document1.ai
inst/manuscript/CDD/revision/Supplementary_Document1.pdf
inst/manuscript/CDD/revision/Supplementary_Document2.pdf
inst/manuscript/CDD/revision/author_contribution_form.pdf
inst/manuscript/CDD/revision/authorsEmailAdresses.txt
inst/manuscript/CDD/revision/reproducibility_checklist_CDD.pdf
inst/recreate_all_figures/recreate_all_figures.Rmd
inst/supp_doc2/supp_doc2.Rmd
inst/supp_doc2/supp_doc2.md
inst/supp_doc2/supp_doc2.pdf
inst/supp_figure1a/supp_figure1a.Rmd
inst/supp_figure1a/supp_figure1a.png
inst/supp_figure1b/supp_figure1b.Rmd
inst/supp_figure1b/supp_figure1b.png
inst/supp_figure2a/supp_figure2a.Rmd
inst/supp_figure2a/supp_figure2a.png
inst/supp_figure2b/polyadenylationMW.ai
inst/supp_figure2b/supp_figure2b.Rmd
inst/supp_figure2b/supp_figure2b.png
inst/supp_figure2c/supp_figure2c.Rmd
inst/supp_figure2c/supp_figure2c.png
inst/supp_figure2c/supp_figure2c.txt
inst/supp_figure2d/supp_figure2d.Rmd
inst/supp_figure2d/supp_figure2d.pdf
inst/supp_figure2e/supp_figure2e.Rmd
inst/supp_figure2e/supp_figure2e.png
inst/supp_figure3a/supp_figure3a.Rmd
inst/supp_figure3a/supp_figure3a.png
inst/supp_figure3b/supp_figure3b.Rmd
inst/supp_figure3b/supp_figure3b.png
inst/supp_figure3c/supp_figure3c.Rmd
inst/supp_figure3c/supp_figure3c.png
inst/supp_figure4a/supp_figure4a.Rmd
inst/supp_figure4a/supp_figure4a.png
inst/supp_figure4b/supp_figure4b.Rmd
inst/supp_figure4b/supp_figure4b.png
inst/supp_figure4c/supp_figure4c.Rmd
inst/supp_figure4c/supp_figure4c.png
inst/supp_figure4d/supp_figure4d.Rmd
inst/supp_figure4d/supp_figure4d.png
inst/supp_figure4d/supp_figure4d_gel.png
inst/supp_figure4d/supp_figure4d_short.ai
inst/supp_figure5a/supp_figure5a.Rmd
inst/supp_figure5a/supp_figure5a.png
inst/supp_figure5b/supp_figure5b.Rmd
inst/supp_figure5b/supp_figure5b.pdf
inst/supp_figure5b/supp_figure5b.png
inst/supp_figure6/supp_figure6.Rmd
inst/supp_figure6/supp_figure6.png
inst/supp_figure7/supp_figure7.Rmd
inst/supp_figure7/supp_figure7.png
inst/supp_figure8/supp_figure8.Rmd
inst/supp_figure8/supp_figure8.png
man/boxplot_stats.Rd
man/calcStats.Rd
man/dct.Rd
man/ddct.Rd
man/figure1c.Rd
man/figure1f.Rd
man/figure2a.Rd
man/figure2b.Rd
man/figure2c.Rd
man/figure2d.Rd
man/figure2e.Rd
man/figure3a.Rd
man/figure3b.Rd
man/figure3c.Rd
man/figure3d.Rd
man/figure4a.Rd
man/fileMap.Rd
man/folds.Rd
man/getCancerColors.Rd
man/getData.Rd
man/get_survival.Rd
man/hPlot.Rd
man/linearStats.Rd
man/mainPlot.Rd
man/pFormat.Rd
man/parseUCSCfiles.Rd
man/plotFigure.Rd
man/plotKM.Rd
man/renderPlots.Rd
man/supp_figure1a.Rd
man/supp_figure2d.Rd
man/supp_figure2e.Rd
man/supp_figure3c.Rd
man/supp_figure4a.Rd
man/supp_figure4c.Rd
man/supp_figure4d.Rd
man/supp_figure5c.Rd
man/supp_figure7.Rd
man/supp_figure8.Rd
man/survival_fit.Rd
man/survival_p.Rd
man/technicalMeans.Rd
man/theme_remove_all.Rd
miR34aFigures.Rproj
vignettes/vignette.Rmd
vignettes/vignette.html
