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Madeline Fontana

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BIOSC 1540 Final Project Report
BIOSC 1540 Final Project Workflow
In-class Exercise: Studying Natural Selection with SNPs
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
Portfolio: PCA Analysis Case Study - Bird Species Morphology
Portfolio: Working with VCF files 4: Imputation of missing data
Portfolio: Working with VCF files 3: Removing samples with many NAs
Software Checkpoint: Loading your VCF file into R
Portfolio: Working with VCF files 2: Removing invariant columns
Portfolio: Working with SNP files 1 - loading and transposing VCF files
Software Checkpoint - Setting a working directory and loading data
Software Checkpoint: vcfR
The vegan package for PCA
BIOSC 1540 In-class Assignment 11/08/2022
PCA and missing data activity in class
BIOSC 1540 RPubs Portfolio - Under the hood of PCA
Under the hood PCA - vegan_PCA_amino_acids portfolio assignment for BIOSC 1540 Computational Biology
Test of RPubs