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
      • Upgrading from a release before 2026.7.6
    • 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
  • Running in parallel
    • How many workers
    • Named clusters
    • Reruns
    • Which tool takes what
  • Binning infrastructure
    • The run definition
      • Reference genome
      • Bins
      • Binner entries
      • Position-score entries
      • Fragment-score entries
        • Modes
        • Two fragments in three bins
        • Uncovered bases
        • Aggregators in each mode
        • The single-cell convention
        • Defaults
        • Empty bins
        • Dropped fragments
        • Grouping by a raw value
        • Local metadata files
      • Track names
      • Coordinates and the grid
    • The output file
    • Reading the file back
    • A worked example
    • Command line tools
  • Command line tools
    • GRR management
      • grr_browse
        • Examples
        • See also
        • Option reference
      • grr_manage
        • Examples
        • See also
        • Option reference
      • grr_cache_repo
        • Examples
        • See also
        • Option reference
    • Annotation
      • annotate_tabular
        • Examples
        • See also
        • Option reference
      • annotate_vcf
        • Examples
        • See also
        • Option reference
      • prepare_tabular
        • Examples
        • See also
        • Option reference
      • annotate_doc
        • Examples
        • See also
        • Option reference
    • Effect annotation
      • annotate_variant_effects
        • Examples
        • See also
        • Option reference
      • annotate_variant_effects_vcf
        • Examples
        • See also
        • Option reference
      • install_vep_cache
        • Examples
        • See also
        • Option reference
    • Binning
      • binning_tool
        • Examples
        • Running the tool
        • See also
        • Option reference
      • Printing a binning file with binning_tool_view
        • Tables
        • Header
        • Selecting bins
        • Selecting tracks
        • Values
        • Option reference
    • Resource utilities
      • draw_score_histograms
        • Examples
        • Option reference
      • to_gpf_gene_models_format
        • Examples
        • Option reference
  • Named clusters
    • The named cluster file
    • The shape of the file
    • How a user file merges with the bundled file
    • Select a cluster on the command line
    • The old key dae_named_cluster
  • GAIn Web interface
    • Create annotation pipelines
    • Add annotators
    • Add resources
    • Registration and user accounts
  • GAIn Python interface
    • Overview and examples
      • 1: Chromosome lengths
      • 2: Position scores across a gene
      • 3: Resource counts by genome
      • 4: Annotating variants in Python
      • 5: Creating an annotator plugin
    • Genomic resources
      • Repositories and resources
        • Accessing a repository
        • Finding a resource
        • Inspecting and reading a resource
        • Closing and refreshing a repository
        • The resource manifest
        • API
      • Reference genomes
        • Accessing a genome
        • Opening and closing a genome
        • Chromosome names and lengths
        • Retrieving DNA sequences
        • Dividing a genome into regions
        • API
      • Gene models
        • Accessing gene models
        • Loading gene models
        • Finding transcripts
        • Working with transcripts and exons
        • Combining and constructing gene models
        • API
      • Genomic scores
        • Accessing a genomic score
        • Opening and closing a genomic score
        • Score definitions
        • Chromosome names and lengths
        • Reading score records and arrays
        • Filtering scores
        • Aggregating scores across regions
        • Score histograms
        • API
      • Position scores
        • Accessing a position score
        • Opening and closing a position score
        • Retrieving position scores
        • Aggregating scores across regions
        • Retrieving scores in bins
        • API
      • Allele scores
        • Accessing an allele score
        • Opening and closing an allele score
        • Retrieving allele scores
        • Aggregating allele scores
        • Multiple records per allele
        • Missing values and filtered results
        • Allele score modes
        • API
      • Fragment scores
        • Accessing a fragment score
        • Opening and closing a fragment score
        • Retrieving fragment scores
        • Aggregating fragment scores
        • Retrieving scores in bins
        • API
      • Gene scores
        • Accessing a gene score
        • Retrieving gene scores
        • Finding genes by score
        • Score definitions and histograms
        • API
      • Histograms
        • Histogram types
        • Reading numeric histograms
        • Reading categorical histograms
        • Reading null histograms
        • Loading histogram files
        • Histogram configuration
        • Categorical limits and truncation
        • API
      • Liftover chains
        • Accessing a liftover chain
        • Opening and closing a liftover chain
        • Converting genomic coordinates
        • Chromosome naming conventions
        • API
      • Gene set collections
        • Accessing a gene set collection
        • Loading a gene set collection
        • Retrieving gene sets
        • Resource formats
        • Gene set statistics
        • API
      • Data frames and AnnData
        • Loading a data frame
        • Loading an AnnData object
        • AnnData file formats
        • Matrix-free loading
        • Backed AnnData objects
        • API
      • Adding new resource types
        • Implementing a resource type
        • Registering a resource type
        • Looking up and registering builders
        • API
    • Annotators
      • What an annotator receives
        • Creating an annotatable
        • The interval
        • Serialised form
        • A None annotatable
        • API
      • What an annotator declares
        • The specification
        • Defaults per attribute
        • The runtime attribute
        • Reading a gene list
        • Aggregation
        • API
      • Writing an annotator
        • The lifecycle
        • What the base does for you
        • Reading parameters
        • The contract
        • Shaping the answer
        • A minimal annotator
        • Annotators that wrap a tool
        • API
      • Testing an annotator
        • Registering in a test
        • A unit test with a seeded context
        • An integration test over a resource
        • What to assert
        • Unsupported fixtures
      • Pipelines
        • Loading a pipeline
        • The lifecycle
        • Running
        • Reading a pipeline
        • Reannotation
        • API
      • Annotator plugins
        • Declaring
        • Discovering
        • Naming in a pipeline
        • The shipped plugins
        • API
    • Task graph
      • Graphs
        • Creating a task graph
        • The lifecycle
        • Task descriptions
        • A running example
        • API
      • Task executors
        • Creating a task executor
        • The lifecycle
        • Running a graph with one call
        • The task cache
        • A running example, part 2
        • API
      • Running from a CLI
        • Creating the arguments
        • The lifecycle
        • A running example, part 3
        • API
      • Named clusters
        • Creating a dask client from a named cluster
        • The lifecycle
        • Where the line falls
        • A running example, part 4
        • API
    • Complete module index
      • gain package
        • Subpackages
        • Submodules
        • gain.logging module
        • Module contents
  • Release Notes
GAIn Documentation
  • Search

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