use TCGAbiolinks_2.29.6 and add psbcSpeedUp

ocbe-uio · Oct 6, 2023 · db02f27 · db02f27
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Supplemental information for ‘Tutorial on survival modelling with omics data’
 
-This is an R Markdown supplement for the article ‘[Tutorial on survival modelling with omics data](https://arxiv.org/abs/2302.12542v1)’, see [here](https://ocbe-uio.github.io/survomics/survomics.html).
+This is an R Markdown supplement for the article ‘[Tutorial on survival modelling with omics data](https://arxiv.org/abs/2302.12542)’, see the step-by-step R tutorial [here](https://ocbe-uio.github.io/survomics/survomics.html).
 
 ## Citation
 

diff --git a/fig/TCGA_adaptivelasso.png b/fig/TCGA_adaptivelasso.png
diff --git a/fig/TCGA_bayesEN.png b/fig/TCGA_bayesEN.png
diff --git a/fig/TCGA_bayesLassoM.png b/fig/TCGA_bayesLassoM.png
diff --git a/fig/TCGA_bayesSpikeSlab.png b/fig/TCGA_bayesSpikeSlab.png
diff --git a/fig/TCGA_bayeslasso.png b/fig/TCGA_bayeslasso.png
diff --git a/fig/TCGA_elastic.png b/fig/TCGA_elastic.png
diff --git a/fig/TCGA_lasso.png b/fig/TCGA_lasso.png
diff --git a/fig/TCGA_surv_auc_lasso.png b/fig/TCGA_surv_auc_lasso.png
diff --git a/fig/TCGA_surv_brier_lasso.png b/fig/TCGA_surv_brier_lasso.png
diff --git a/fig/TCGA_surv_brier_t_lasso.png b/fig/TCGA_surv_brier_t_lasso.png
diff --git a/fig/TCGA_surv_calibration.png b/fig/TCGA_surv_calibration.png
diff --git a/fig/TCGA_surv_cindex_lasso.png b/fig/TCGA_surv_cindex_lasso.png
diff --git a/fig/TCGA_surv_iauc_lasso.png b/fig/TCGA_surv_iauc_lasso.png
diff --git a/fig/TCGA_surv_km_lasso.png b/fig/TCGA_surv_km_lasso.png
diff --git a/fig/TCGA_surv_nomogram.png b/fig/TCGA_surv_nomogram.png
diff --git a/fig/TCGA_surv_roc.png b/fig/TCGA_surv_roc.png
diff --git a/fig/mlr3_calibration_BS.png b/fig/mlr3_calibration_BS.png
diff --git a/fig/mlr3_calibration_RCLL.png b/fig/mlr3_calibration_RCLL.png
diff --git a/fig/mlr3_discrimination_msrs.png b/fig/mlr3_discrimination_msrs.png
diff --git a/references.bib b/references.bib
@@ -406,4 +406,20 @@ @misc{Sonabend2022
   eprint        = {2212.05260},
   archiveprefix = {arXiv},
   primaryclass  = {math.ST}
+}
+
+@article{Zucknick2023,
+  title   = {Penalized Semiparametric {Bayesian} Survival Models},
+  author  = {Manuela Zucknick, Zhi Zhao, Maral Saadati, Axel Benner},
+  year    = 2023,
+  journal = {R package version 2.0.},
+  volume  = {\url{https://github.com/ocbe-uio/psbcSpeedUp.git} (18 September 2023, date last accessed)}
+}
+
+@article{Zhao2023,
+  title   = {Penalized Semiparametric Bayesian Survival Models},
+  author  = {Zhi Zhao and Manuela Zucknick and Maral Saadati and Axel Benner},
+  year    = 2023,
+  journal = {R package version 2.0.4.},
+  volume  = {\url{https://CRAN.R-project.org/package=psbcSpeedUp}}
 }
diff --git a/survomics.Rmd b/survomics.Rmd
diff --git a/survomics.html b/survomics.html