Publications by Thomas
CompBio_Bio
R Markdown My name is Thomas Ku. I am from Glendora, California. I am currently a sophomore student at the University of Pittsburgh who is planning to major in Computational Biology, though I am not sure exactly what in Computational Biology. Rather than a biology background, I come from a more computer science based background, and have been wor...
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CompBio_2020
R Markdown This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com. When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within t...
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Distance Matrix Building
Preliminaries ##install.packages("ape") ##install.packages("phangorn") library(ape) library(phangorn) ##Summary on Obtaining Data The data for Example 2, or 5 sequences of genetic DNA was obtained by looking at multiple sequence pair alignments of five chimpanzee species in Africa. These 5 species were Mahale East, Bodongo East, Gombe East, T...
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Computational Biology: Population Viability Analysis
Data: Figure 5 (plus 10 years) Make data vectors, calculate lambda, and put together dataframe with all necessary data. census The census period; an index from 1 to 39 of how many years of data have been collected. census <- 1:39 year t The year: 1959 to 1997 (Dennis et al use 1959-1987) year.t <- 1959:1997 Population size Population size is...
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Tree Functions
Assignment: unrooted trees We often don’t root phylogenetic trees. This reduces the number of possible trees and is described by the equation: Text: (2n-5)!/[2n-3*(n-3)!] Rendered: \(\frac{(2*n-5)!}{2^{n-3} * (n-3)!}\) Assignment part 1 Modify the function used in the “number of phylogenetic trees” tutorial to work for unrooted trees. Comp...
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Replicating Higgs and Attwood’s analysis on the properties of amino acids
INTRODUCTION: This script analyzes data on amino acids and attempts to replicate work done by Higgs and Attwood. This script analyzes correlations and similarities between amino acids to see how they function together in protein folding. Analysis of amino acids using bioinformatics is important since protein folding is a vital piece in the functi...
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Building Data frames in R
Introduction This exercise is meant to challenge you to build a dataframe by hand in R. It is based off of the Table 1 in Drake (1991) “A constant rate of spontaneous mutation in DNA-base microbes” (PNAS August 15, 1991 88 (16) 7160-7164; https://doi.org/10.1073/pnas.88.16.7160) There are two parts to this tutorial. This versions will guide y...
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