Publications by Leila Dean Stansberry
Final Portfolio Assignment- SLC22A5
Introduction The SLC22A5 gene provides instructions for making a protein called OCTN2 that is found in the heart, liver, muscle, kidneys, and other tissues. The gene is also known to code for a protein, solute carrier family 22 member 5. Mutations may cause systemic primary carnitine deficiency (CDSP). Sodium-ion dependent, high affinity carnitin...
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FAQ: How do I add a line of best fit to a scatterplot in ggpubr?
QUESTION: “How do I add a line of best fit to a scatterplot in ggpubr?” If you have a 2D scatterplot, how do you add a line of best fit to the graph using ggpubr? Data We’ll use the “palmerpenguins” packages (https://allisonhorst.github.io/palmerpenguins/) to address this question. You’ll need to install the package with install.pack...
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Predicting amino acid properties using regression
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...
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Pairwise global alignment of DNA sequences using the Needleman-Wunsch algorithm
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_0012...
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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(rentrez) library(compbio4all) library(Biostrings) ## Loading required package: BiocGenerics ## Loading required package: parallel ## ## Attaching package: 'BiocGenerics' ## The following objects are masked from 'package:parallel': ## ## clusterAp...
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Using R to investigate gene SLC22A5 for sequence 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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Adjusting dotplot setting 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 dotplots 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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Downloading DNA sequences as FASTA files 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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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/leila/Downloads" Copy and paste the current wd in the code chunk b...
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