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+title: "Resources"
+output: html_document
+---
+
+### About
+
+[R]These walkthroughs were created by Aaron Mitchell-Dick.  They are based off of vignettes from source packages (see links to package vignettes/walkthroughs below).  These walkthroughs are intended to aid beginning knowledge in bioinformatics and display commenting on common techniques an advanced user would already know.  In addition to these, there are a lot of other great resources for beginniners that do not necessitate hard lessons in coding. For example [Galaxy](https://galaxyproject.org) is an excellent resource for the entire bioinformatics community, and it's free.  Any questions or commments please email aaron.mitchell.dick@duke.edu.  Enjoy!
+
+### Links to vignettes and repositories mentioned in the walkthroughs on this website:
+
+1. [kallisto](https://pachterlab.github.io/kallisto/)
+2. [tximport](https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html)
+3. [DESeq2](http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html)
+4. [TrimGalore](https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md)
+5. [FastQC](https://raw.githubusercontent.com/s-andrews/FastQC/master/INSTALL.txt) and [FastQC website](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+
+Other helpful links:
+
+6. [kallisto indices and tarballs containing .gtf files]
+7. [github repo to fork to create your own website like this]
+
+8. The definitive guide for all things R Markdown [https://bookdown.org/yihui/rmarkdown/](https://bookdown.org/yihui/rmarkdown/)
+
+This website was created by forking the [original project from Matt Crump](https://github.com/CrumpLab/LabJournalWebsite) and the instructional [YouTube video to set up your own webpage](https://www.youtube.com/watch?v=nc7XhQrasCM). 
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-
-### R and R-Studio
-
-[R](http://www.r-project.org) is a free open-source programming language that can be used for statistical analysis, data-simulation, graphing, and lots of other stuff. Another free program is [R-studio](http://www.rstudio.com), that provides a nice graphic interface for R. Download R first, then download R-studio. Both can run on PCs, Macs or Linux. Students will be learning R in the stats labs using the lab manual []().
-
-### Additional R resources
-
-1. Google is great, Google your problem
-2. [Stackoverflow](https://stackoverflow.com) is great, google will often take you there because someone has already asked your question, and someone else has answered, usually many people have answered your question many ways.
-3. Danielle Navarro wrote a [free Psych Stats textbook using R](https://compcogscisydney.org/learning-statistics-with-r/), it's worth checking out (some of our textbook are based on Danielle's)
-4. I am currently writing another stats textbook (incorporating some of the above). You can read it while it's being made right here [https://crumplab.github.io/statistics/](https://crumplab.github.io/statistics/), also check out the lab manual for more specific things about doing various stats in R (also in draft right now) [https://crumplab.github.io/statisticsLab/](https://crumplab.github.io/statisticsLab/)
-5. Daniell Navarro recently made this website for introducing R, it's great, check it out (also made using this R markdown process): [http://compcogscisydney.org/psyr/](http://compcogscisydney.org/psyr/)
-6. Check out my slightly older programming book that also introduces R [https://crumplab.github.io/programmingforpsych/](https://crumplab.github.io/programmingforpsych/)
-7. This is the definitive guide for all things R Markdown (you will find this very useful as you get better at this skill): [https://bookdown.org/yihui/rmarkdown/](https://bookdown.org/yihui/rmarkdown/)
-