Statistical Genetics and Genomics

  1. Computational Tools and Resources
    1. Software Packages
      1. R Packages for Genetics
        1. genetics
          1. SNPassoc
            1. GenABEL
              1. GWAS Tools
              2. Python Libraries
                1. PyVCF
                  1. scikit-allel
                  2. Specialized Software
                    1. GCTA
                      1. BOLT-LMM
                        1. SAIGE
                      2. Databases and Resources
                        1. Genotype Databases
                          1. dbSNP
                            1. 1000 Genomes Project
                              1. gnomAD
                                1. UK Biobank
                                2. Phenotype Databases
                                  1. GWAS Catalog
                                    1. ClinVar
                                      1. OMIM
                                        1. PhenoScanner
                                        2. Functional Databases
                                          1. Ensembl
                                            1. UCSC Genome Browser
                                              1. GTEx Portal
                                                1. ENCODE
                                              2. High-Performance Computing
                                                1. Cluster Computing
                                                  1. Job Scheduling
                                                    1. Parallel Processing
                                                      1. Memory Management
                                                      2. Cloud Computing
                                                        1. AWS for Genomics
                                                          1. Google Cloud Platform
                                                            1. Data Security Considerations
                                                            2. Workflow Management
                                                              1. Nextflow
                                                                1. Snakemake
                                                                  1. WDL
                                                                2. Data Management
                                                                  1. File Formats
                                                                    1. VCF Format
                                                                      1. BGEN Format
                                                                        1. Hail MatrixTable
                                                                        2. Data Storage
                                                                          1. Compression Methods
                                                                            1. Indexing Strategies
                                                                              1. Backup Procedures
                                                                              2. Data Sharing
                                                                                1. FAIR Principles
                                                                                  1. Privacy Protection

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                                                                              10. Specialized Applications

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                                                                              1. Foundations of Statistical Genetics