rrprem
Rhea Premanand
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Final Project Workflow - Rhea Premanand
This is the full workflow for the final project.
Final Project Report - Rhea Premanand
This is the cleaned up final project report that loads in the scaled data and performs pca analysis on it.
In Class Exercise: Studying Natural Selection with SNPs
fst_exploration_in_class-STUDENT.Rmd
Worked Example Part 2: Data Analysis
PCA on SNPs data form a vcf file
10-PCA_worked_example-SNPs-part2.Rmd
Worked Example Part 1: Data Preparation
PCA on SNPs data from a .vcf file
09-PCA_worked_example-SNPs-part1.Rmd
PCA Analysis Case Study - Bird Species Morphology
Portfolio
08-PCA_worked.Rmd
Working with VCF Files 4: Imputation of Missing Data
07-mean-imputation.Rmd
Working with VCF files 3: Removing samples with many NAs
bird_snps_remove_NAs.Rmd
Portfolio
Removing Fixed Alleles from SNP Data
removing_fixed_alleles.Rmd
Preparing VCF data for Analysis: Transportation
12/2/22
transpose_VCF_data.Rmd
Setting a working directory and loading data
working_directory_practice with walsh_2017_morphology data
Software Checkpoint: vcfR
code_checkpoint_vcfR
vegan_pca_with_msleep-STUDENT
RPubs Portfolio: the vegan package and PCA
Under the Hood of PCA
Portfolio Assignment with vegan_PCA_amino_acids-STUDENT.Rmd file
Temp
Software Checkpoint: RPubs