Publications by Leila Dean Stansberry
A Bioinformatics Flow
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...
6837 sym R (13511 sym/58 pcs) 1 img
A Bioinformatics Flow
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...
6865 sym R (13515 sym/58 pcs) 1 img
Genomics is failing in diversity graphs
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...
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Accessing data from Google Docs
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 download a list of RefSeq accessions from a Google sheet remove the NAs using na.omit() select out all but one isoform using duplicated() Packages...
867 sym R (2919 sym/27 pcs)
Accessing data from Google Docs
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 (TODO: MAKE YOUR OWN OUTLINE) Packages ## Google sheets download package # comment this out when you are done # install.packages("googlesheets4")...
5632 sym R (18022 sym/124 pcs) 1 img
ggplot2 and ggpubr test
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...
4282 sym R (2501 sym/35 pcs) 9 img
FAQ: What makes for a good data dictionary, and ...make one in R?
QUESTION: “What makes for a good data dictionary, and …make one in R?” Data We’ll use the “palmerpenguins” packages (https://allisonhorst.github.io/palmerpenguins/) to address this question. What makes a good dictionary? A good dictionary includes columns and labels that are self-explanatory when the user/reader can easily read somet...
503 sym R (804 sym/4 pcs) 1 tbl
How do I make a 3D scatterplot in R?
QUESTION: “How do I make a 3D scatterplot in R?” 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.packages(“palmerpenguins”) if you have not done so before, call library(“palmerpenguins”), and load the data w...
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How do I do a pairwise sequence alignment in R?
QUESTION: “How do I do a pairwise sequence alignment in R?” If you have a protein sequence, how do you do a pairwise alignment in R? Data Preparation We will use the data created below to address this question. You will need install the packages by install.packages(“compbio4all”), install.packages(“rentrez”), and install.packages(“...
1144 sym R (5169 sym/53 pcs)
FAQ: How do I display a multiple sequence alignment using ggmsa?
QUESTION: “How do I do a pairwise sequence alignment in R?” If you have protein sequences from different species, how do you do a pairwise alignment to compare them in R? Data Preparation We will use the data created below to address this question. You will need install the packages by install.packages(“compbio4all”), install.packages(�...
1384 sym R (3999 sym/34 pcs) 1 img