├── .gitignore ├── Chapter01 ├── Interfacing_R.py ├── R_magic.py ├── base_setup.sh └── bioinformatics_base.txt ├── Chapter02 ├── .gitignore ├── Arrow.py ├── Matplotlib.py ├── NumPy.py ├── Pandas_Basic.py ├── Pandas_Join.py └── Pandas_Memory.py ├── Chapter03 ├── Accessing_Databases.py ├── Basic_Sequence_Processing.py ├── Filtering_SNPs.py ├── LCT.bed ├── Processing_BED_with_HTSeq.py ├── Working_with_BAM.py ├── Working_with_FASTQ.py └── Working_with_VCF.py ├── Chapter04 ├── 2L.py ├── Exploration.py ├── Mendel.py ├── Preparation.py ├── QIIME2_Metagenomics.py └── samples.tsv ├── Chapter05 ├── .gitignore ├── Annotations.py ├── Gene_Ontology.py ├── Getting_Gene.py ├── Low_Quality.py ├── Orthology.py └── Reference_Genome.py ├── Chapter06 ├── .gitignore ├── Admixture.py ├── Data_Formats.py ├── Exploratory_Analysis.py ├── PCA.py ├── Pop_Stats.py └── Sgkit.py ├── Chapter07 ├── .gitignore ├── Alignment.py ├── Comparison.py ├── Exploration.py ├── Reconstruction.py ├── Selection.py ├── Trees.py └── Visualization.py ├── Chapter08 ├── .gitignore ├── Distance.py ├── Intro.py ├── Mass.py ├── PDB.py ├── Parser.py ├── PyMol_Intro.py ├── PyMol_Movie.py ├── Stats.py └── mmCIF.py ├── Chapter09 ├── galaxy │ ├── .gitignore │ ├── LCT.bed │ ├── api.py │ ├── encrypt.py │ └── galaxy.yaml ├── nextflow │ ├── .gitignore │ └── pipeline.nf └── snakemake │ ├── .gitignore │ ├── Snakefile │ └── plot_pca.py ├── Chapter10 ├── Clustering.py ├── Decision_Tree.py ├── PCA.py └── Random_Forest.py ├── Chapter11 ├── .gitignore ├── Dask_Distributed.py ├── Dask_Intro.py ├── MP_intro.py └── Zarr_Intro.py ├── Chapter12 ├── Builtin.py ├── Lazy.py ├── Mutability.py ├── Persistence1.py ├── Persistence2.py ├── Pure.py ├── Recursion.py ├── Tools.py ├── my_genes.csv └── my_genes.csv.base ├── Datasets.py ├── LICENSE ├── README.md ├── Welcome.ipynb └── docker ├── Chapter01 └── Dockerfile └── main └── Dockerfile /.gitignore: -------------------------------------------------------------------------------- 1 | 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