Publications by Evan Gu
Downloading, cleaning, and aligning data- evg16
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 Packages library(googlesheets4) # comp bio packages library(seqinr) library(rentrez) library(compbio4all) library(Biostrings) ## Loading requ...
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Pie Graph Assignment
Introduction The pie graphs show the proportion of races of people used in genomic studies. The data was collected by the Genomic-Wide Association Studies. It was collected by analyzing sample descriptions included in the GWAS Catalog. The process was repeated in 2016 to see if there was any change in the proportion of races of people used in gen...
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Investigating your shroom for the presence of repeats
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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Using dotplots in R to investigate sequence repeats
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...
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Introduction to Dot Plots 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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Evan Gu- 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/evang/Downloads" Copy and paste the current wd in the code chunk b...
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MSA Walkthrough Assignment
Assignment: Your assignment is to use your notes from class - along with help from classmates, UTAs, and me - to turn this script into a fleshed-out description of what is going on. This is a substantial project - we’ll work on it in steps over the rest of the unit. We are currently focused on the overall process and will cover the details over...
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CompBio-EvanGu-Portfolio
Assignment: Your assignment is to use your notes from class - along with help from classmates, UTAs, and me - to turn this script into a fleshed-out description of what is going on. This is a substantial project - we’ll work on it in steps over the rest of the unit. We are currently focused on the overall process and will cover the details over...
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Download FASTA 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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Using R to investigate gene LRRC19 for sequence repeates
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...
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