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profbiot

Jessica Kaufman

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Plot MS Spectra
Document
MicrobiomeThesis2024
Merging Tutorial
Learn how to download data with R and merge with existing file.
Example Final Script
Filter Example
Week 2 shortcut
Here is a shortcut to completing 4/5 assignments in one step
Species Level Taxonomic Bar Plot
Here are some tips and tricks to cut down the number of species and format your taxonomic bar plot.
GetTopProteins
Very similar to the script we used to find top species for the microbiome project. Here we read in and clean up MaxQuant results to produce a list of the top ten proteins found in our samples.
Intro to Tidy
Phenotype Search Example
read.GenBank tutorial
Parse Galaxy BLAST Results
Index FASTA file
Filter All Levels
Guide script for systematically filtering a Kraken2 report by classification level.
Too Many Species to Plot
This script is an optional set of steps for students who have too many species to represent on a bar plot.
Example Box Plot
This quick tutorial shows how to structure tidy data and make a boxplot colored by group of data.
Pie Charts on US Map
Points on US Map
US Map Plotting
Get Top 5 Species
Use dplyr to quickly find highest 5 counts in a taxonomic report for microbiome analysis.
FilterSpecies
FilterSpecies
Intro to reading and writing in RStudio
Read in data from Spotify charts and export to csv file without the URL column.