├── .gitignore ├── Chapter01 ├── Interfacing_R.ipynb ├── R_magic.ipynb └── example.png ├── Chapter02 ├── Accessing_Databases.ipynb ├── Basic_Sequence_Processing.ipynb ├── Filtering_SNPs.ipynb ├── LCT.bed ├── Processing_BED_with_HTSeq.ipynb ├── Working_with_BAM.ipynb ├── Working_with_FASTQ.ipynb ├── Working_with_VCF.ipynb └── example.png ├── Chapter03 ├── Annotations.ipynb ├── Gene_Ontology.ipynb ├── Getting_Gene.ipynb ├── Low_Quality.ipynb ├── Orthology.ipynb ├── Reference_Genome.ipynb └── example.png ├── Chapter04 ├── Admixture.ipynb ├── Data_Formats.ipynb ├── Exploratory_Analysis.ipynb ├── F-stats.ipynb ├── Genepop_Format.ipynb ├── PCA.ipynb ├── admix.2 ├── admix.3 ├── admix.4 ├── admix.5 ├── admix.6 ├── admix.7 ├── admix.8 ├── admix.9 ├── example.png ├── hapmap10_auto_noofs_ld.2.P ├── hapmap10_auto_noofs_ld.2.Q ├── hapmap10_auto_noofs_ld.3.P ├── hapmap10_auto_noofs_ld.3.Q ├── hapmap10_auto_noofs_ld.4.P ├── hapmap10_auto_noofs_ld.4.Q ├── hapmap10_auto_noofs_ld.5.P ├── 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