Publications by Maia Lim
Portfolio 1-Maia Lim
A complete bioinformatics workflow in R By: Nathan L. Brouwer “Worked example: Building a phylogeny in R” Introduction Phylogenetics uses tools such as sequence alignment and phylogenetic trees to gain further understanding on evolution and the relationships between species. Computational phylogenetics is thus important for carrying out ali...
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test
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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Portfolio: 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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Investigating your focal gene for the presence of repeats
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...
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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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Needle Comparison
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: Q9CD83 hom...
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post exam 4 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...
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