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index.Rmd
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---
title: "Sequencing & Bioinformatics Resources"
permalink: /
author: "Author: Linton Freund ([email protected])"
date: "Last update: `r format(Sys.time(), '%d %B, %Y')`"
output:
html_document:
toc: true # table of content true
toc_depth: 3 # upto three depths of headings (specified by #, ## and ###)
number_sections: false ## if you want number sections at each table header
theme: cosmo # many options for theme, see here: https://www.datadreaming.org/post/r-markdown-theme-gallery/
highlight: pygments # specifies the syntax highlighting style
code_folding: show
toc_float: true
collapsed: true
smooth_scroll: true
fontsize: 15pt
always_allow_html: yes
---
<style type="text/css">
body{
font-size: 13pt;
}
</style>
<!--
Render from R:
rmarkdown::render_site(encoding = 'UTF-8')
* Need index.html and _site.yml and all other Rmd files in same directory to build full website
Rendering from the command-line. To render to PDF format, use the argument setting: output_format="pdf_document".
$ Rscript -e "rmarkdown::render_site(encoding = 'UTF-8')"
Add logo:
htmltools::img(src = knitr::image_uri("mylogo.png"),
alt = 'logo',
style = 'position:absolute; top:0; center:0; padding:10px;')
NOTE:
If you add any files to your website, you MUST update your _site.yml and _config.yml files to include this info!
-->
Hello, and welcome to my page that is all about sequencing, bioinformatics, data science,and all things 'omics!
# My Background
My name is Linton Freund, my pronouns are they/them, and I am a PhD Candidate at the University of California Riverside. I am in the [Genetics, Genomics, and Bioinformatics PhD Program](https://ggb.ucr.edu/) and a member of Dr. Emma Aronson's lab.
I earned my Masters in Biology from California State University Long Beach in 2019. As a member of The Bioinformatics Lab led by Dr. Renaud Berlemont, I used shotgun metagenomic sequencing and bioinformatic tools to examine the gut microbial community from cartilaginous fishes. You can find my masters thesis [here](https://www.proquest.com/dissertations-theses/insights-into-structure-function-gut-metagenome/docview/2294094842/se-2).
I am currently focusing on the characterization of soil, water, and aeolian (i.e. wind-driven dust) microbiomes as well as microbiome-microbiome interactions within the Salton Sea, CA. To learn more about this ecosystem and these microbiomes, please check out our literature review on the topic [here](https://escholarship.org/uc/item/8br2r9k9).
<center>
</center>
<div align="center">An Example of My Current Project's Workflow</div></br>
For some personal information about me, please feel free to see my profile on [500 Queer Scientists](https://500queerscientists.com/hannah-freund/?ids=[5381]).
# Other Helpful Resources
Here are some of my favorite resources for learning more about coding, bioinformatics, statistics, and sequence analysis.
* [Happy Belly Bioinformatics](https://astrobiomike.github.io/)
* [DADA2 Pipeline Tutorial](https://benjjneb.github.io/dada2/tutorial.html)
* [Dr. Mike Lee's Microbial Omics Slack Channel](https://join.slack.com/t/microbialomics/shared_invite/zt-hewufeet-RTgCOf8TnfCUbIP2_GdQUg)
* [Biostars](https://www.biostars.org/)
* [Stackoverflow](https://stackoverflow.com/)
* [Happy Git and Github for the userR](https://happygitwithr.com/)
* [R for Data Science](https://r4ds.had.co.nz/)
* [R Markdown Website Tutorial](https://www.emilyzabor.com/tutorials/rmarkdown_websites_tutorial.html)
* [The Analysis of Biological Data w/ R](https://whitlockschluter.zoology.ubc.ca/r-code)
* [Be awesome in ggplot2](http://www.sthda.com/english/wiki/be-awesome-in-ggplot2-a-practical-guide-to-be-highly-effective-r-software-and-data-visualization#geom_text-textual-annotations)
* [Software Carpentry's Intro to Python](https://swcarpentry.github.io/python-novice-inflammation/setup.html)
* [Bash Guide: Commands & Arguments](http://mywiki.wooledge.org/BashGuide/CommandsAndArguments)
* [Bash Scripting Cheatsheet](https://devhints.io/bash)
* [StatQuest with Josh Starmer](https://www.youtube.com/c/joshstarmer)
# Awesome Organizations to Join and/or Support
* [Black Girls Code](https://www.blackgirlscode.com/)
* [Out in STEM](https://ostem.org/)
* [International Society of Nonbinary Scientists](https://isnbs.org/)
* [Women in Data Science](https://www.widsconference.org/)
* [R-Ladies Global](https://rladies.org/)
<div align="center">**Thanks for stopping by!**</div>
<center>
[](https://hlfreund.github.io/)
</center>