Publications by Nathan Brouwer
Adjusting Dotplot Settings in R
In this exercise we’ll look at a sequence with known tandem repeats. We’ll load the data, explore it in R, then use the dotPlot() function to make various dotplots to see how changing settings for dotPlots() help make repeat patterns stand out. Add the necessary code to make this script functional. Preliminaries Load packages library(seqinr...
1550 sym R (7611 sym/73 pcs) 12 img
Investigating APOL1 for Repeats
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': ## ## clusterApply, clusterApplyLB, clusterCall, clu...
926 sym R (6417 sym/37 pcs) 5 img
Downloading, Cleaning, and Aligning Data
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 Load necessary packages Download our outside data from google docs Process the data Setting up the process Using code to input 2 sequences to be ali...
5187 sym R (18135 sym/124 pcs) 1 img
Post Test Assignment
gpubr - allometric data Allometric data - classic case of regression, using logs, using non-linear model too library(compbio4all) Vocab wrapper ggplot2 ggpubr $ operator smoother continous data categorical data Learning objectives Know what a wrapper is Know the relationship between ggplot2 and ggpubr Be able to run code that makes graphs wit...
4282 sym R (2503 sym/35 pcs) 9 img
Predicting Amino Acid Characteristics Using Regression Models
Key vocab proteinogenic amino acids regression model / line of best fit pI confidence intervals (CI) confidence ellipse correlation coefficient Selenocysteine and Pyrrolysine re-coding stop codons y = m*x + b slope intercept Key functions / packages ggpubr pander lm() coef() cor() round() Predict pI for an Selenocysteine and Pyrrolysine Amino...
5802 sym R (6116 sym/42 pcs) 1 img 4 tbl
Final Portfolio
Introduction The Apolipoprotein 1 gene, better known as APOL1, is a protein involved in processes around the kidneys and liver. Genetic mutations in this gene have been found to be cause of kidney diseases. The following code will give a detailed summary of the properties, phylogenies, alignments, and evolutionary characteristics of the APOL1 gen...
3283 sym R (40648 sym/211 pcs) 9 img 6 tbl