COVID-19 Variants Analysis

This is a two-part project for analyzing genetic variations in SARS-CoV-2, a virus responsible for COVID-19/Coronavirus. The project was done with R, and it focuses on sequences across samples from different countries.

Target

1. Analyze and compare gene sequence from differente SARS-CoV-2 samples.
2. Identify mutations across individual and country-level samples.
3. Visualize the similarities and differences using R tools.

Project Structure

• Evidencia1: This contains the individual sequence analysis.
• Evidencia2: This contains the comparations of the sequence analysis between countries.

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Tools & Packages

This project was developed using R and requires the following packages:

• Biostrings
• tidyverse
• ggplot2
• msa
• ape
• ggtree

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How to Run Evidencia1

Prerequisites

Make sure you have R and RStudio installed. Then install the required packages (if not already installed):

install.packages("tidyverse")
install.packages("ggplot2")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("Biostrings", "msa", "ggtree", "ape"))

1. Open ev01.Rmd in RStudio.
2. Click "Knit" to generate the HTML report.
3. Alternatively, run Evidencia1_codigo.R line by line to step through the analysis.

How to Run Evidencia2

1. Open ev02.Rmd in RStudio.
2. Click "Knit" to generate the HTML report.