ALLYSON DEMERLIS
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Coding

Not only is coding challenging, but it requires a steep learning curve to get acclimated and comfortable with. However, it is also an essential part of research nowadays - at the very least using a statistical software or data visualization tool. Here is a list of links to workshops, tutorials, YouTube videos, and more that I have found thus far in my graduate school research while trying to learn all these programs and languages. I hope these may be of help to you. 

Introduction to Coding
  • Software Carpentry designs workshops specifically for teaching research computing: https://software-carpentry.org/
  • Data Carpentry designs workshops for data-driven research: https://datacarpentry.org/

Introduction to R
Online Courses/Workshops
  • RStudio resources for beginners: https://education.rstudio.com/learn/beginner/
  • Learn R, in R! An interactive tutorial - I HIGHLY RECOMMEND: https://swirlstats.com/
  • StatQuest for all things statistical analyses AND DNA/RNA sequencing! What a pro!  https://statquest.org/video-index/
  • Coursera free online course on R programming: https://www.coursera.org/learn/r-programming
  • A fun R advent calendar, "25 Days of R" for an intro: https://kiirstio.wixsite.com/kowen/post/the-25-days-of-christmas-an-r-advent-calendar
  • Harvard Introduction to R Workshop: http://tutorials.iq.harvard.edu/R/Rintro/Rintro.html
  • Rmarkdown tutorial: https://ourcodingclub.github.io/tutorials/rmarkdown/
  • Interactive tutorial called "learnr" 
    • filter( ): https://learnr-examples.shinyapps.io/ex-data-filter/
    • summarise( ): https://learnr-examples.shinyapps.io/ex-data-summarise/#section-summarise-groups-with-summarise​

Free Books!
  • Fundamentals of Data Visualization by Claus Wilke: https://serialmentor.com/dataviz/
  • R for Data Science by Garrett Grolemund and Hadley Wickham: https://r4ds.had.co.nz/

Online Coding Club - Amazing resource with step-by-step R code for tidying data and data visualization!
  • ​https://ourcodingclub.github.io/

DNA/RNA Sequencing 
Informative Articles
  • How Next-Generation Sequencing works: https://www.illumina.com/science/technology/next-generation-sequencing/beginners/ngs-workflow.html
  • A great overview to the experimental design, sample prep, and downstream analysis of RNA sequencing data: https://rnaseq.uoregon.edu/
    • Differential Expression software comparisons: https://rnaseq.uoregon.edu/#table5.2

Workshops
  • Data Wrangling and Processing for Genomics - Data Carpentry workshop: https://datacarpentry.org/wrangling-genomics/
    • Requires knowledge of bash + use of terminal
    • Assessing read quality of FASTQ, trimming and filtering sequences, variant calling
  • Harvard Chan Bioinformatics Core Differential Gene Expression Workshop: https://github.com/hbctraining/DGE_workshop/tree/master/lessons 
  • RNA-sequencing data analysis workshop: https://github.com/hbctraining/Intro-to-rnaseq-hpc-O2
    • the shell, vim, quality assessment, alignment with STAR, generating counts matrix, multiqc, salmon
  • Differential Expression analysis code: https://github.com/mistrm82/msu_ngs2015/blob/master/hands-on.Rmd
    • Comparison of DESeq2, EdgeR, and limma
    • YouTube tutorial that goes through the entire code with an explanation: https://www.youtube.com/watch?v=7UKMU5HK380
  • Using awk (Unix tool) to analyze a transcriptome: http://reasoniamhere.com/2013/09/16/awk-gtf-how-to-analyze-a-transcriptome-like-a-pro-part-1/

YouTube Videos
  • Beginner's Guide to RNA-Seq webinar: https://www.youtube.com/watch?v=8lAVfKbRK3I
  • Canadian Bioinformatics Workshop on RNA Sequencing: https://www.youtube.com/watch?v=Ji9nFCYl7Bk
  • RNA-seq results explained: https://www.youtube.com/watch?v=9Xo1HU_H828



Last updated: June 15, 2025
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  • Home
  • Publications
  • Press
  • Research
    • University of Miami
    • Mote Marine Laboratory
  • CV
  • Resources
    • Grad School
    • Coding
    • Jobs
  • Photography
    • Corals Close-Up
    • Coral Fluorescence
    • Bonaire
    • The Florida Keys
    • Miami
  • Talks
  • Contact
  • Online Lab Notebook