Publications by Bhuvitha Chagantipati
FAQ: How do I make a scatterplot matrix from a dataframe or matrix?
Question: How do I make a scatterplot matrix from a dataframe or matrix? 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�...
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Final Portfolio
Introduction This code compiles summary information about the gene HFE(Homeostatic Iron Regulator). It also generates alignments and a phylogeneitc tree to indicating the evolutionary relationship betweeen the human version of the gene and its homologs in other species. Resources/References RefSeq Gene: https://www.ncbi.nlm.nih.gov/gene/3077 Ref...
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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...
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Pairwise alignment
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_000401....
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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 Packages ## Google sheets download package # install.packages("googlesheets4") library(googlesheets4) # comp bio packages library(seqinr) library...
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Testing Google Sheets Access
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...
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Pie Chart
Introduction Alice B. Popejoy and Stephanie M. Fullerton collected data to support that certain drugs may be less effective, or even unsafe, in some populations because of genetic differences. To determine ancestry, they analysed the sample descriptions included in the GWAS Catalog with an approach similar to that used in 2009. Data was collected...
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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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Bioinformatics Workflow
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...
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Investigating Shroom for 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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