Publications by Deeksha Sesha
Extra Credit 5
QUESTION: How do you carry out principle components analysis (PCA) using the princomp() function, and plot the results? I will show how to conduct PCA with princomp(), which is a fucntion in base R to carry out PCA. prcomp() is another function in base R that is also used for PCA. Data We’ll use the “palmerpenguins” packages (https://allis...
1354 sym R (2355 sym/11 pcs) 3 img
Extra Credit 4
QUESTION: How do you make a diagram of the protein DIO1 using the drawProteins package? Preparation Loading Necessary Packages library(BiocManager) ## Bioconductor version '3.13' is out-of-date; the current release version '3.14' ## is available with R version '4.1'; see https://bioconductor.org/install library(ggplot2) library(drawProteins) ...
737 sym R (3187 sym/13 pcs) 1 img 2 tbl
Extra Credit 4
QUESTION: How do you make a diagram of the protein DIO1 using the drawProteins package? Preparation Loading Necessary Packages library(BiocManager) ## Bioconductor version '3.13' is out-of-date; the current release version '3.14' ## is available with R version '4.1'; see https://bioconductor.org/install library(ggplot2) library(drawProteins) ...
546 sym R (3187 sym/13 pcs) 1 img 2 tbl
Extra Credit 1
QUESTION: How do you make boxplots using ggpubr? There are multiple methods you can use tu can make boxplots in R. Here, I will demonstrate how to make a boxplot using the ggpubr package. Data We’ll use the “palmerpenguins” packages (https://allisonhorst.github.io/palmerpenguins/) to address this question. You’ll need to install the pack...
1217 sym R (374 sym/7 pcs) 1 img
Document
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 (4481 sym/27 pcs) 1 img 4 tbl
Testing ggplot2 and ggpubr
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 (2474 sym/35 pcs) 9 img
Accessing Google Sheets Data
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...
865 sym R (2756 sym/25 pcs)
Pie Graphs Part 1
Introduction The data that is plotted represents the percentage of people participating in genome-wide association studies (GWAS) who are of European, Asian, and other non-European descents. Summaries from GWAS studies are available in the GWAS catalog, which is produced by the US National Human Genome Research Institute and the European Bioinfor...
1905 sym R (968 sym/3 pcs) 1 img
Using R to Investigate Gene SLC24A5 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...
1601 sym R (6131 sym/35 pcs) 5 img
Investigating Shroom3 For the Presence of 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': ## ## ...
1193 sym R (6199 sym/37 pcs) 5 img