Publications by Deeksha Sesha
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] "/Users/dsesha02/Desktop/OneDrive - University of Pittsburgh/des217" Copy and...
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Portfolio1PartA-D
A complete bioinformatics workflow in R Code By: Nathan L. Brouwer “Worked example: Building a phylogeny in R” Introduction In biology, phylogenies can be used to study evolutionary relationships among different species of organisms. Phylogenies can be made using morphological data or molecular data (nucleic acids or proteins). Scientists u...
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Downloading 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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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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Adjusting Dotplot Settings 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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Unit 4 Review Portfolio Assignment
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") l...
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Pairwise Alignment Portfolio
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_995322....
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Extra Credit 2
QUESTION: How do you make a scatterplot with color coding in ggpubr? Here I will demonstrate how to add color coding using both a categorical and a continuous variable. 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.pa...
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Extra Credit 3
QUESTION: How do you scale and center a single column in a dataframe? Data scaling refers to the process of taking each element in a column of data from a dataframe and dividing each point by the standard deviation. Data centering refers to the process of subtracting the mean of the elements in the column from each ppoint. I will demonstrate how ...
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SLC24A5: Final Portfolio
Final Portfolio Assignment: SLC24A5 - Sodium/potassium/calcium exchanger 5 Code By: Deeksha Sesha Introduction This code compiles summary information about the gene SLC24A5 (Sodium/potassium/calcium exchanger 5). SLC24A5 codes for the Sodium/potassium/calcium exchanger 5 protein, which is very important for skin pigmentation. In addition to show...
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