Publications by Bhuvitha Chagantipati
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...
12658 sym R (2120 sym/40 pcs)
Using R to investigate gene XXXX for sequence repeates
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...
1609 sym R (5914 sym/35 pcs) 5 img
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 Copy and paste the current wd in the code chunk below behind a comment so it won’t run as ...
1707 sym R (117 sym/3 pcs)
Adjusting dotplot setting in R to investigate sequence repeats in Shroom
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...
1527 sym R (6617 sym/50 pcs) 12 img
Using dotplots in R to investigate sequence repeats Start Assignment
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...
1609 sym R (5914 sym/35 pcs) 5 img
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...
5649 sym R (3412 sym/22 pcs) 1 img 4 tbl
Portfolio 1: Assignment C
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...
11865 sym R (20764 sym/94 pcs) 6 img
FAQ: How do carry out cluster analysis in R?
Question: How do carry out cluster analysis 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...
401 sym R (1049 sym/8 pcs) 2 img