Publications by Rashi Ranjan
TRPM8 Case Study
Introduction Transient receptor potential cation channel subfamily M (melastatin) member 8 (TRPM8) is a protein that is coded for by the TRPM8 gene. The gene codes for cold-sensing TRP channel that is activated by chemical ligands such as menthol and icilin; it is the primary molecular transducer for cold somatosensation in humans. Resources & R...
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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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Global proteins alignments in R
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). Code specific to the TRPM8 gene for humans and mice. Preliminaries library(compbio4all) library(Biostrings) Download sequences As we did in the previous lesson on dotplots, we’ll look a...
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Replicating Pie Charts in R
Introduction Alice B. Popejoy and Stephanie M. Fullerton from the University of Washington (at the time of publishing, 2016) collected data on genome-wide association studies (GWAS) conducted until 2016, in which they studied what populations were involved in GWASs. They collected this data by extracting and validating English-language GWASs repo...
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Using R to investigate gene TRPM8 for sequence repeats
Change the TRPM8 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...
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Adjusting dotplot setting 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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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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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...
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Rashi's bioinformatics workflow in R
A complete bioinformatics workflow in R By: Nathan L. Brouwer, adapted by Rashi Ranjan “Worked example: Building a phylogeny in R” Introduction Phylogenies can be used to show changing relationships between groups of organisms, exemplifying the similarities and differences between them. Phylogenetic trees use the concept to show evolutionar...
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first rmd :)
R Markdown This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com. When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within t...
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