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RhettRautsaw/README.md

Rhett M. Rautsaw, Ph.D.

Evolution | Ecology | Conservation | Genomics | Bioinformatics

Welcome to my GitHub Page!

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Who am I?

Generally I am interested developing and using tools that transform complex genomic data into biological knowledge. I consider myself an integrative/computational biologist with interests spanning the intersection of evolution, ecology, genomics, and conservation. Specifically, I use high-throughput sequencing methods and bioinformatics to understand (1) how ecology and changes in the genome impact the evolution of traits and (2) how genetic and trait diversity can impact our conservation decisions. For my Ph.D., I used hundreds of high-throughput sequencing samples to study the phylogenomics of vipers 🐍 and role of competition on the evolution of their venom. While at USF/WSU for my postdoc, I will be working on Tasmanian Devil Facial Tumor Disease genomics; examining how the tumor has evolved since its divergence from the parental Tasmanian Devil genome.

Experience

I have 8+ years of experience in bioinformatics, statistics, scripting/programming, software engineering, pipeline development, application development, high-throughput sequencing data analysis, and scientific communication. I have experience in a variety of -omic methodolgies including Illumina short-read transcriptomics (RNA-Seq), ATAC-Sequencing, Whole-Genome Bisulfite-Sequencing (Methylation Sequencing), and PacBio SMRT HiFi Sequencing.

What am I learning now?

  • Deep Learning
  • Docker
  • Snakemake
  • C++
  • HTML/Javascript

Repositories

Below you will find a list of the repositories, tutorials, workshops, scripts, and applications I have developed...and yes I have way too much fun making GitHub repositories.

Pipelines & Scripts

Shiny Apps

I have a Digital Ocean Server on which I host several Shiny Apps (RhettRautsaw.app)

Tutorials/Workshops

GitHub Stats

Rhett's GitHub stats Top Langs

Citations

@mmistakes minimal-mistakes Jekyll Theme.

Pinned

  1. Bioinformatics Bioinformatics Public

    This repository contains many simple, but potentially useful bioinformatics scripts as well as functions and resources for improving your skillset and performing really cool analyses.

    Python 8 1

  2. MitoSIS MitoSIS Public

    MitoSIS (Mitochondrial Species Identification System) is a wrapper for mitochondrial genome assembly and identification of sample contamination or mislabeling.

    Python 4 1

  3. VenomMaps VenomMaps Public

    Distribution maps and niche models for venomous snakes.

    R 11 2

  4. SequencingEstimator SequencingEstimator Public

    This Shiny App is designed to help you estimate sequencing needs and costs on various platforms.

    R 3

  5. GIS_Tutorial GIS_Tutorial Public

    The basics of GIS, qGIS, and R with tips, tricks, and resources

    Python 1

  6. CoordinateMapper CoordinateMapper Public

    Shiny app to quickly plot latitude/longitude points via copy-paste from spreadsheet.

    R 3