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Eesha Mukherjee

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Final Project Workup (Pt1)
Final Report: Analysis of 1000 Genomes Data with PCA
Final project for this class
Worked Example: PCA on SNPs data from a vcf file Part 2 - Data Analysis
Worked Example: PCA on SNPs data from a vcf file Part 1 - Data Preparation
PCA Analysis Case Study - Bird Species Morphology
Mean imputation of missing data in R
Working with VCF files 3: Removing samples with many NAsusing for loops
Studying natural selection with SNPs
Removing Fixed Allels from SNP data
Working with SNP files 1 - loading and transposing VCF files
Setting a working directory in R
The vegan package for PCA
Code Check Point: Testing vcfR
Please complete the following Software checkpoint to make sure you can work with .vcf files in R on your computer. Take notes on what is done in this workflow. You will have to load a .vcf file on the final exam. Note that this is due MONDAY after the break before we meet again. Work through this .Rmd file, add the necessary code, and post to Rpubs. 2022-11-18
Under the Hood PCA
Getting Started Using RPubs
Starting assignment for Rpubs (Comp Bio 1500)