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About and References.Rmd
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---
title: "About and References"
output: html_document
---
# About
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 be thorough enough that a user with beginning knowledge in bioinformatics can perform RNA-Seq analysis from scratch. They 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 [email protected]. 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](https://github.com/pachterlab/kallisto-transcriptome-indices/releases)
7. [github repo to fork to create your own website like this](https://github.com/CrumpLab/LabJournalWebsite)
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).