GAIn Documentation
Contents:
Getting started on the web
Select annotation pipeline
Single annotatable
Annotation jobs
Getting started on CLI
Installation
Browse available resources
Simple annotation pipeline
Annotating tabular input
Annotating VCF input
Annotating positions and regions
Parallelization []
Reannotation
Getting started with GRR
Create your first GRR
Add new resources
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 CNV collection
13: CNV collection (Iossifov 2021)
Select GRR to work with
miniGRR: a template GRR
Genomic resources and repositories
Repository discovery
Repository configuration
Repository caching
Repository management
Genomic resource configuration
Genomes
Gene models
Liftover chains
Annotation pipelines
Position scores
table
scores
default_annotation
Allele scores
CNV collections
Gene scores
Gene set collections
Histogram configuration
VCF score auto-detection
Tabix indexing
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
cnv_collection_annotator
gene_set_annotator
spliceai_annotator
VEP annotators
vep_full_annotator
external_vep_gtf_annotator
Command line tools
Notes on usage
annotate_columns
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. CNV collection annotation
7: Gene set annotation
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
GAIn Development
gain package
Subpackages
gain.annotation package
gain.dask package
gain.effect_annotation package
gain.gene_scores package
gain.gene_sets package
gain.genomic_resources package
gain.task_graph package
gain.testing package
gain.utils package
Module contents
GAIn Documentation
Annotators Plugin Library
View page source
Annotators Plugin Library