Publications by Hersh Parikh
How do I make a distance matrix in R?
QUESTION: How do I make a distance matrix in R? How do make a distance matrix in R using data. 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(...
944 sym R (1220496 sym/5 pcs)
Calculating frequency of each amino acid in a polypeptide sequence
Preparation Necessary libraries library(compbio4all) library(rentrez) library(seqinr) Data A table of accession numbers dio1_table<-c("NP_000783", "P49895","NA","Homo sapiens" , "Human", "DIO1", "NP_001116123","NA", "NA", "Pan troglodytes" , "Chimpanzee","DIO1", "NP_031886", "Q61153","NA","Mus musculus...
309 sym R (1530 sym/7 pcs)
Parse Function in FASTA Cleaner
Preparation Necessary libraries library(compbio4all) library(rentrez) library(seqinr) Data A table of accession numbers dio1_table<-c("NP_000783", "P49895","NA","Homo sapiens" , "Human", "DIO1", "NP_001116123","NA", "NA", "Pan troglodytes" , "Chimpanzee","DIO1", "NP_031886", "Q61153","NA","Mus musculus...
352 sym R (2937 sym/8 pcs)
How do I check if two vectors are identical to each other?
QUESTION: How do I check if two vectors are identical to each other? If you have two vectors, how do you know if they are identical? 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 ...
1049 sym R (2057 sym/4 pcs)
How do I make a basic data table from a vector?
QUESTION: How do I make a basic data table from a vector? If you have a vector in R, how do you make a data table from it? 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 d...
971 sym R (174 sym/4 pcs) 1 tbl
Final portfolio assignment: BRINP3 gene – BMP/retinoic acid inducible neural specific 3
Introduction This code contains summary information about the BRINP3 gene, which encodes the BMP/retinoic acid inducible neural specific 3 protein. It also builds an MSA and phylogenetic tree to show the evolutionary relationship between the human version of this gene and its homologs in other species. Resources / References Key information use ...
2638 sym R (31571 sym/136 pcs) 6 img 9 tbl
Study Guide Part 1
Setup Install any needed packages. #install.packages("lsa") #install.packages("mdendro") #install.packages("dendextend") Load all packages # packages we've used a lot library(ggplot2) library(ggpubr) # packages we've only recently started using library(scatterplot3d) library(pander) library(vegan) ## Loading required package: permute ## Loading...
3213 sym R (28781 sym/115 pcs) 8 img 3 tbl
ggpubr/ggplot2 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 (2471 sym/35 pcs) 9 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 getwd() ## [1] "/Users/Hersh/Desktop" Copy and paste the current wd in the code chunk below ...
1801 sym R (336 sym/4 pcs)
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...
4562 sym R (12835 sym/54 pcs) 1 img