adding links to all pages to each index page because i can't get the …

…damn dropdown menus to work on mobile :(

R/index.md

@@ -11,11 +11,20 @@ permalink: /R/
 [R](https://www.r-project.org/) is generally a big, glorious calculator. More specifically, it's a programming language and working environment for statistical analyses and figure generation, and it's pretty sweet. What really makes R powerful is that it is completely open source and it has a tremendous number of incredible people that contribute "packages" to it for all to use. Packages are bundles of code that perform specific tasks, and they are kinda like Apps in the sense that for most of the things you'll want to do, "there's a package for that". Often you will end up searching for a package that you know exists already either from hearing about it from someone, or seeing it used in a paper, but you can also search the [Comprehensive R Archive Network (CRAN) for packages](https://cran.r-project.org/web/packages/) directly. R serves as the foundation upon which you can utilize this large swath of tools that people all over the world have developed and contributed, and it also is invaluable for parsing tables and creating figures. It's definitely worth the initial time investment it may take to get comfortable with it.  
 
 There is extensive documentation on R at the CRAN [Introduction to R site](https://cran.r-project.org/doc/manuals/r-release/R-intro.html), and it would probably be worthwhile going through it at some point. Consistent with the general approach of the site here, I try to distill things down to just the baseline skills to start in the [R basics]({{ site.url }}/R/basics) page.  
+
 <br>
 
 ---
 <br>
+# R pages
+* [Introduction to R](/R/basics)  
+* [Going deeper with indexing](/R/more_indexing)  
+* [Installing R packages](/R/installing_packages)  
+
+<hr style="height:10px; visibility:hidden;" />
 
+---
+<br>
 <h3>Some terminology</h3>
 
 **Variable**  

amplicon/index.md

@@ -15,6 +15,21 @@ Don't get too lost in the weeds when working with marker-gene data. More often t
 
 <p align="right"><a href="https://ndownloader.figshare.com/files/15628100">PDF download</a></p>
 
+<hr style="height:10px; visibility:hidden;" />
+
+---
+<br>
+# Amplicon pages
+
+* [Demultiplexing example](/amplicon/demultiplexing)  
+* [A full walkthrough of processing and initial analyses](/amplicon/dada2_workflow_ex)  
+* [An example of dealing with 16S and 18S mixed together](/amplicon/16S_and_18S_mixed)  
+
+<hr style="height:10px; visibility:hidden;" />
+
+---
+<br>
+
 **Amplicons and marker-genes and tags, oh my!**  
 Most often a marker-gene analysis is the microbial ecologist's first tool in a vast toolkit. It is primarily used as a broad survey of community structure. As the warning notes above, when first beginning to work with this type of data it can be easy to get caught spinning your wheels about a subtle component in your processing pipeline that ultimately has a negligible impact compared to the noise we are working through. What I mean by this is, generally speaking, tag sequencing is most often not the appropriate tool to answer really meticulous questions. It is a tool for comparing baseline *proxies* of metrics about microbial communities. It is a tool of exploration and hypothesis generation.  
 

genomics/index.md

@@ -12,3 +12,13 @@ categories: [genomics]
 <p align="right"><a href="https://ndownloader.figshare.com/files/15628103">PDF download</a></p>
 
 Genomics is a very broad subject. In my small bubble, my time spent in the genomics realm involves mostly working with bacteria and archaea doing things like assembly, functional annotation, assessing distributions across metagenomes, comparative genomics, and trying to infer evolutionary relationships through phylogenomics. But as usual there are a ton of questions to pursue and lots of ways to pursue them. Here I'm going to provide some examples of some of the things I do 🙂
+
+<hr style="height:10px; visibility:hidden;" />
+
+---
+<br>
+# Genomics pages
+
+* [Where to start: quality filtering, error correction, and depth normalization](/genomics/where_to_start)  
+* [*de novo* genome assembly](/genomics/de_novo_assembly) 
+* [Recovering **M**etagenome-**A**ssembled **G**enomes (MAGs) from metagenomes](/genomics/metagen_anvio)