Publications by Nathan Brouwer
Accessing Data from Google Docs
The goal of this exercise is to make you familiar with how to download data from Google Sheets and to briefly review some key concepts R functions and coding concepts. We’ll do the following things download a list of RefSeq accessions from a Google sheet remove the NAs using na.omit() select out all but one isoform using duplicated() Packages...
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FAQ: Adding a Correlation Coefficient to a Scatterplot Using ggpubr
QUESTION: How do I add a correlation coefficient to my scatterplot when I use ggpubr/ggscatter? To do this, we simply add a small argument into the function. Data We’ll use the “palmerpenguins” packages (https://allisonhorst.github.io/palmerpenguins/) to address this question. You’ll need to install the package with install.packages(“p...
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Global Alignment
Global proteins aligments in R By: Avril Coghlan. Adapted, edited and expanded: Nathan Brouwer under the Creative Commons 3.0 Attribution License (CC BY 3.0). Preliminaries library(compbio4all) library(Biostrings) Download sequences As we did in the previous lesson on dotplots, we’ll look at two sequences. # Download ## sequence 1: APOL1 Hu...
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Replicating Pie Graphs
Introduction The data shown in the following pie graphs is from the paper “Genomics is Failing on Diversity” written by Alice B. Popejoy and Stephanie M. Fullerton. They were investigating the proportions of different ethnicities and their representation in Genome-Wide Association Studies, where in 2009, 96% of data came from individuals of E...
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Investigating Shroom
Add the necessary code to make this script function. Preliminaries Load packages library(seqinr) library(rentrez) library(compbio4all) library(Biostrings) ## Loading required package: BiocGenerics ## Loading required package: parallel ## ## Attaching package: 'BiocGenerics' ## The following objects are masked from 'package:parallel': ## ...
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Dotplots in R
Sequence dotplots in R By: Avril Coghlan. Adapted, edited and expanded: Nathan Brouwer under the Creative Commons 3.0 Attribution License (CC BY 3.0). NOTE: I’ve added some new material that is rather terse and lacks explication. Good sources of more info: https://omicstutorials.com/interpreting-dot-plot-bioinformatics-with-an-example/ http://r...
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APOL1 Gene Fasta File in R
This is a modification of “DNA Sequence Statistics” from Avril Coghlan’s A little book of R for bioinformatics.. Most of the text and code was originally written by Dr. Coghlan and distributed under the Creative Commons 3.0 license. NOTE: There is some redundancy in this current draft that needs to be eliminated. Functions library() help...
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Working Directory Test
Default working directory Open up this .Rmd file in RStudio. In the code chunk below type getwd() and run it. “wd” means “working directory”, or where R will currently save files if you tell it to save anything. # Get the current working directory getwd() ## [1] "C:/Users/fropo/Downloads" Copy and paste the current wd in the code chunk b...
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Bioinformatics Workflow
Introduction In biology, phylogenies are used to create a phylogenetic tree that can then be further analyzed. Vocab Multiple Sequence Alignment (MSA) phylogenetic tree fasta file pairwise alignment shroom gene packages cat distance matrix percent identity (PID) list Key functions rentrez::entrez_fetch Biostrings::pairwiseAlignment devtools::in...
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Working Directory Test
Default working directory Open up this .Rmd file in RStudio. In the code chunk below type getwd() and run it. “wd” means “working directory”, or where R will currently save files if you tell it to save anything. # Get the current working directory getwd() ## [1] "C:/Users/fropo/University of Pittsburgh/compbio2021 - ktd16" Copy and paste...
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