GAIn Documentation

Contents:

  • Getting started on the web
    • Select annotation pipeline
    • Single annotation
    • Annotation jobs
    • Custom annotation pipeline
  • Getting started on CLI
    • Prerequisites
    • Installation
    • Browse available resources
    • Quick annotation test
    • Custom annotation pipelines
    • Using the VEP effect annotator
    • Caching resources
    • Parallelizing large annotation jobs
    • Annotating VCF input
    • Annotating positions and regions
    • Adding public GRRs
    • Adding local GRRs
    • Reannotation
  • Getting started with GRR
    • Create your first GRR
    • Connect the local GRR to GAIn
    • Add new resources to the local GRR
      • 1: Toy genome
      • 2: Genome (GRCh38.p14)
      • 3: Gene models (MANE v1.4)
      • 4: Toy position score
      • 5: Position score (PhyloP7)
      • 6: Toy allele score
      • 7: Allele score (AlphaMissense)
      • 8: Toy gene score
      • 9: Gene score (pLI)
      • 10: Toy gene sets
      • 11: Gene sets (MSigDB)
      • 12: Toy fragment score
      • 13: Fragment score (Iossifov 2021)
    • Browse the local GRR
    • Annotate using the local GRR
    • mini-GRR: a template GRR
  • Genomic resources and repositories
    • Repository discovery
    • Repository configuration
      • Common fields
      • Repository types
    • Repository caching
    • Complete GRR definition example
    • Repository management
      • grr_manage
        • Rebuilding on demand: --force and --dry-run
      • grr_browse
    • Searching resources
      • The search index
      • Indexed fields
      • Searching by label
      • List-valued labels
      • Limitations
    • Version control for GRRs
      • Initializing version control
      • Adding a resource to version control
      • Metadata-only updates
    • Genomic resource configuration
      • Genomes
      • Gene models
      • Liftover chains
      • Annotation pipelines
      • Position scores
        • table
        • scores
        • default_annotation
      • Score value types
      • Allele scores
      • Fragment scores
      • Gene scores
      • Gene set collections
    • Histogram configuration
    • VCF score auto-detection
    • Tabix indexing
  • GRR configuration files
    • How the CLI tools find the configuration
    • Configuration file structure
      • Common fields
      • Repository types
      • Search order
    • Resource caching
    • A complete annotated example
  • Annotation infrastructure
    • Annotation pipelines
    • Preamble
    • Annotators
      • Score annotators
        • position_score_annotator
        • allele_score_annotator
        • gene_score_annotator
      • Effect annotators
        • effect_annotator
        • simple_effect_annotator
      • Transforming annotators
        • liftover_annotator
        • normalize_allele_annotator
        • chrom_mapping
      • fragment_score_annotator
        • Requiring a substantial overlap
      • gene_set_annotator
      • spliceai_annotator
      • VEP annotators
        • vep_full_annotator
        • vep_effect_annotator
    • Command line tools
      • Notes on usage
      • annotate_tabular
      • annotate_vcf
      • annotate_doc
    • Example annotations
      • 1: Effect annotation
      • 2: Position score annotation
      • 3: Allele score annotation
      • 4: Gene score annotation
      • 5: Liftover annotation
      • 6. Fragment score annotation (CNVs)
      • 7: Gene set annotation
  • Binning position scores with binning_tool
    • The run definition
      • Reference genome
      • Bins
      • Binner entries
      • Track names
      • Coordinates and the grid
    • Running the tool
      • Dry run
      • Parallelism
      • Work directory and reruns
    • The output file
    • Reading the file back
    • A worked example
  • GAIn Web interface
    • Create annotation pipelines
    • Add annotators
    • Add resources
    • Registration and user accounts
  • Annotators Plugin Library
  • GAIn Python interface
    • 1: Chromosome lengths
    • 2: Position scores across a gene
    • 3: Resource counts by genome
    • 4: Annotating variants in Python
    • 5: Creating an annotator plugin
  • GAIn Development
    • Working with resources in Python
      • Where the line falls
      • The shape of the API
        • Repositories and resources
        • Reference genomes
        • Gene models
        • Scores
        • Histograms
        • Adding a resource type
      • Not covered here
    • Complete module index
      • gain package
        • Subpackages
        • Submodules
        • gain.logging module
        • Module contents
  • Release Notes
GAIn Documentation
  • Search

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