Man pages for GranderLab/miR34a_asRNA_project
The miR34AasRNAproject package facilitates the transparency and reproducibility of the miR34a asRNA project and associated publication.
| boxplot_stats | Calculate boxplot stats |
| calcStats | calcStats |
| dct | dct |
| ddct | ddct |
| figure1c | miR34a asRNA and miR34a TCGA correlation. |
| figure1f | Conding potential analysis via CPAT. |
| figure2a | miR34a asRNA expression in HCT116 and HEK293t upon... |
| figure2b | miR34a asRNA doxorubicin treatment of HCT116 p53 wt and null. |
| figure2c | P1 transfections in HCT116 and HEK293t cells. |
| figure2d | miR34a asRNA siRNA KD. |
| figure2e | P1 transfections with shRNA Renilla and doxorubicin... |
| figure3a | miR34a asRNA stable over-expression cell lines. |
| figure3b | miR34a asRNA PC3 stable cell line cell cycle. |
| figure3c | Monitoring growth of miR34a asRNA overexpressings cells under... |
| figure3d | PC3 stable line pollII ChIP. |
| figure4a | TCGA survival analysis |
| fileMap | fileMap |
| folds | folds |
| getCancerColors | Colors for survival plot. |
| getData | getData |
| get_survival | Calculate survival object |
| hPlot | Plots the survival boxplot inset and p-value. |
| linearStats | Calculate correlation stats |
| mainPlot | Plots the survival scatterplot. |
| parseUCSCfiles | parseUCSCfiles |
| pFormat | pFormat |
| plotFigure | plotFigure |
| plotKM | Plots KM plots |
| renderPlots | Renders the scatter plot with the boxplot as an inset. |
| supp_figure1a | TCGA correlation table. |
| supp_figure2d | ENCODE RNAseq data for the cellular localization analysis. |
| supp_figure2e | Conding potential analysis via CPC. |
| supp_figure3c | P1 shRenilla HEK293t transfections. |
| supp_figure4a | miR34a asRNA stable over-expression cell lines compared to... |
| supp_figure4c | CCND1 expression in PC3 stable cell lines. |
| supp_figure4d | CCND1 protein expression in PC3 stable lines. |
| supp_figure5c | Monitoring proliferation of miR34a asRNA overexpressings... |
| supp_figure7 | lnc34a splice junction analysis. |
| supp_figure8 | lnc34a CAGE analysis. |
| survival_fit | Calculate survival fit |
| survival_p | Calculate survival p-value |
| technicalMeans | technicalMeans |
| theme_remove_all | Theme for survival plot. |
