About and References.Rmd

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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).