Publications by Nathan Brouwer
Using R to investigate gene Lag3 for sequence repeates
Change the XXXXX of the title to your gene name. Change the names and text appropriately to reflect your gene / protein. Add the necessary code to make this script functional. Download the PROTEIN sequence of your gene. Adapting the code below, make 2 grids of 4 plots (8 plots total) exploring different settings for window size and the match thre...
1603 sym R (5929 sym/35 pcs) 5 img
Pie chart of genomic study diversity
Assignment information: (delete this when you submit) In this assignment you will re-build the pie graphs shown in the paper “Genomics is failing on diversity” by Popejoy and Fullerton (https://www.nature.com/articles/538161a). Delete all instructions and replace with short explanatory text about all code chunks. Be sure to change the title i...
1924 sym R (904 sym/3 pcs) 1 img
Global proteins aligments in R
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: NP_002277....
11069 sym R (8751 sym/68 pcs)
Predicting amino acid chemistry 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...
5647 sym R (3164 sym/20 pcs) 1 img 4 tbl
LAG3 Protein Structure Analysis
Introduction LAG3 (Lymphocyte activation gene 3 protein) functions as an inhibitory receptor on antigen activated T-cells. It delivers inhibitory signals when bound to ligands. Resources / references Human protein: https://www.ncbi.nlm.nih.gov/search/all/?term=NP_002277.4 Homologene: https://www.ncbi.nlm.nih.gov/homologene/?term=lag3 Uniprot: ht...
1533 sym R (21487 sym/87 pcs) 6 img 5 tbl