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Intro
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Classroom Contents
Genes and Geography - A Bioinformatics Project
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- 1 Intro
- 2 Hunting for data
- 3 Inspecting the VCF
- 4 Finding population labels for the samples
- 5 Parsing VCF with pysam
- 6 Going from alleles to numbers for a numpy array
- 7 When to work in colab versus python script
- 8 Saving data with pandas
- 9 Adding population labels from the panel file
- 10 To Colab!
- 11 PCA
- 12 First plot! Mission accomplished :
- 13 Using Altair for plotting with labels
- 14 Second plot with population labels!
- 15 Merging with the igsr_population.tsv data
- 16 TSNE
- 17 Exercise: PCA on the SNPs
- 18 Conclusion and origin story for this project
