6 files changed, 109 insertions, 0 deletions
diff --git a/lit-review-template.qmd b/lit-review-template.qmd
new file mode 100644
index 0000000..3329a3d
--- /dev/null
+++ b/lit-review-template.qmd
@@ -0,0 +1,52 @@
+---
+title: "TEMPLATE_FIELD"
+author: "TEMPLATE_FIELD"
+date: now
+date-format: "DD MMMM YYYY - HH:mm"
+format:
+  pdf:
+    toc: false
+    number-sections: true
+    fig-caption: yes
+    highlight-style: "zenburn"
+    include-in-header:
+    - text: |
+        \usepackage{etoolbox}
+
+        \AtEndPreamble{\hypersetup{colorlinks=true,linkcolor=blue,urlcolor=blue,citecolor=red}}
+    extra-dependencies:
+      - float
+      - multicol
+
+bibliography: references.bib
+link-citations: true
+editor-options:
+  markdown:
+    wrap: 72
+---
+
+\tableofcontents
+\newpage
+
+<!-- If you have a number of topics, subdivide them in sections and organize papers under them -->
+# Topic one
+
+## Paper one [@Shin_2014]
+
+## Paper two [@Suhre_2011]
+
+# Topic two
+
+\newpage
+
+<!-- Add youtube channels and databse links here -->
+# Online resources
+
+\newpage
+
+<!-- For listing and defining new vocabulary -->
+# Glossary
+
+\newpage
+
+# References
diff --git a/lit-review-template.rmd b/lit-review-template.rmd
new file mode 100644
index 0000000..3ad65f3
--- /dev/null
+++ b/lit-review-template.rmd
@@ -0,0 +1,46 @@
+---
+title: "TEMPLATE_FIELD"
+author: "TEMPLATE_FIELD"
+date: "`r format(Sys.time(), '%d %B %Y - %H:%M')`"
+output:
+  pdf_document:
+    toc: false
+    number_sections: true
+    fig_caption: yes
+    highlight: "zenburn"
+    extra_dependencies: ['float','multicol']
+bibliography: references.bib
+link-citations: true
+header-includes:
+  - \usepackage{etoolbox}
+  - \AtEndPreamble{\hypersetup{colorlinks=true,linkcolor=blue,urlcolor=blue,citecolor=red}}
+editor_options:
+  markdown:
+    wrap: 72
+---
+
+\tableofcontents
+\newpage
+
+<!-- If you have a number of topics, subdivide them in sections and organize papers under them -->
+# Topic one
+
+## Paper one [@Shin_2014]
+
+## Paper two [@Suhre_2011]
+
+# Topic two
+
+\newpage
+
+<!-- Add youtube channels and databse links here -->
+# Online resources
+
+\newpage
+
+<!-- For listing and defining new vocabulary -->
+# Glossary
+
+\newpage
+
+# References
diff --git a/references.bib b/references.bib
new file mode 100644
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--- /dev/null
+++ b/references.bib
@@ -0,0 +1,2 @@
+@article{Shin_2014, title={An atlas of genetic influences on human blood metabolites}, volume={46}, ISSN={1546-1718}, url={http://dx.doi.org/10.1038/ng.2982}, DOI={10.1038/ng.2982}, number={6}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={ and Shin, So-Youn and Fauman, Eric B and Petersen, Ann-Kristin and Krumsiek, Jan and Santos, Rita and Huang, Jie and Arnold, Matthias and Erte, Idil and Forgetta, Vincenzo and Yang, Tsun-Po and Walter, Klaudia and Menni, Cristina and Chen, Lu and Vasquez, Louella and Valdes, Ana M and Hyde, Craig L and Wang, Vicky and Ziemek, Daniel and Roberts, Phoebe and Xi, Li and Grundberg, Elin and Waldenberger, Melanie and Richards, J Brent and Mohney, Robert P and Milburn, Michael V and John, Sally L and Trimmer, Jeff and Theis, Fabian J and Overington, John P and Suhre, Karsten and Brosnan, M Julia and Gieger, Christian and Kastenmüller, Gabi and Spector, Tim D and Soranzo, Nicole}, year={2014}, month=May, pages={543–550} }
+@article{Suhre_2011, title={Human metabolic individuality in biomedical and pharmaceutical research}, volume={477}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature10354}, DOI={10.1038/nature10354}, number={7362}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={ and Suhre, Karsten and Shin, So-Youn and Petersen, Ann-Kristin and Mohney, Robert P. and Meredith, David and Wägele, Brigitte and Altmaier, Elisabeth and Deloukas, Panos and Erdmann, Jeanette and Grundberg, Elin and Hammond, Christopher J. and de Angelis, Martin Hrabé and Kastenmüller, Gabi and Köttgen, Anna and Kronenberg, Florian and Mangino, Massimo and Meisinger, Christa and Meitinger, Thomas and Mewes, Hans-Werner and Milburn, Michael V. and Prehn, Cornelia and Raffler, Johannes and Ried, Janina S. and Römisch-Margl, Werner and Samani, Nilesh J. and Small, Kerrin S. and -Erich Wichmann, H. and Zhai, Guangju and Illig, Thomas and Spector, Tim D. and Adamski, Jerzy and Soranzo, Nicole and Gieger, Christian}, year={2011}, month=Aug, pages={54–60} }
diff --git a/scripts/doi2bib b/scripts/doi2bib
new file mode 100755
index 0000000..358c728
--- /dev/null
+++ b/scripts/doi2bib
@@ -0,0 +1,5 @@
+#!/bin/sh
+case "$1" in
+	*"doi.org"*) curl -LH "Accept: application/x-bibtex" $1;;
+	*) curl -LH "Accept: application/x-bibtex" "https://doi.org/$1";;
+esac
diff --git a/scripts/qmd2pdf b/scripts/qmd2pdf
new file mode 100755
index 0000000..4442b34
--- /dev/null
+++ b/scripts/qmd2pdf
@@ -0,0 +1,2 @@
+#!/bin/sh
+quarto render "$1"
diff --git a/scripts/rmd2pdf b/scripts/rmd2pdf
new file mode 100755
index 0000000..3c7a287
--- /dev/null
+++ b/scripts/rmd2pdf
@@ -0,0 +1,2 @@
+#!/bin/sh
+Rscript -e "rmarkdown::render('$1')"