In ramiromagno/ensemblr: R Client for the Ensembl REST API

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The list of Ensembl REST API endpoints can be found at https://rest.ensembl.org/. Below you will find the current coverage of Ensembl REST API endpoints by {ensemblr}.

Coverage

| Ensembl REST API Section | Coverage | | ---------------- | ---------------- | | Archive | 2/2 | | Comparative genomics | 0/12 | | Cross references | 2/3 | | eQTL | 3/3 | | Information | 10/26 | | Linkage disequilibrium | 3/3 | | Lookup | 0/4 | | Mapping | 0/4 | | Ontologies and taxonomy | 0/8 | | Overlap | 0/3 | | Phenotype annotations | 0/4 | | Regulation | 0/7 | | Sequence | 0/4 | | Transcript Haplotypes | 0/1 | | VEP | 0/6 | | Variation | 0/6 | | Variation GA4GH | 0/22 |

Archive

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET archive/id/:id | get_id() | Get details about an Ensembl identifier. | | POST archive/id | --- | Get details about an Ensembl identifier. |

Comparative genomics

| Ensembl REST API | {ensemblr} API | Description | | --------------------------------------------------- | ---------------- | ----------- | | GET cafe/genetree/id/:id | --- | --- | | GET cafe/genetree/member/id/:id | --- | --- | | GET cafe/genetree/member/symbol/:species/:symbol | --- | --- | | GET family/id/:id | --- | --- | | GET family/member/id/:id | --- | --- | | GET family/member/symbol/:species/:symbol | --- | --- | | GET genetree/id/:id | --- | --- | | GET genetree/member/id/:id | --- | --- | | GET genetree/member/symbol/:species/:symbol | --- | --- | | GET alignment/region/:species/:region | --- | --- | | GET homology/id/:id | --- | --- | | GET homology/symbol/:species/:symbol | --- | --- |

Cross references

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET xrefs/symbol/:species/:symbol | --- | --- | | GET xrefs/id/:id | get_xrefs_by_ensembl_id() | --- | | GET xrefs/name/:species/:name | get_xrefs_by_gene() | --- |

eQTL

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET eqtl/id/:species/:stable_id | get_eqtl_pval_by_gene() | Retrieve eQTLs associated with queried gene. | | GET eqtl/variant_name/:species/:variant_name | get_eqtl_pval_by_variant() | Retrieve genes eQTL associated with queried variant. | | GET eqtl/tissue/:species | get_eqtl_tissues() | Returns all tissues currently available in the eQTL database. |

Information

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET info/analysis/:species | get_analyses() | Gets a table of analyses involved in the generation of data for the different Ensembl databases. | | GET info/assembly/:species | get_assemblies() get_toplevel_sequences() get_karyotypes() get_cytogenetic_bands() | Genome assembly level information, such as toplevel sequences, karyotype and cytogenetic bands. | | GET info/assembly/:species/:region_name | get_toplevel_sequence_info() | Get a few extra details about a toplevel sequence. | | GET info/biotypes/:species | --- | --- | | GET info/biotypes/groups/:group/:object_type | --- | --- | | GET info/biotypes/name/:name/:object_type | --- | --- | | GET info/compara/methods | --- | --- | | GET info/compara/species_sets/:method | --- | --- | | GET info/comparas | --- | --- | | GET info/data | get_data_versions() | Get data release version(s) available on the Ensembl REST server. | | GET info/eg_version | get_ensembl_genomes_version() | Get Ensembl Genomes database version. | | GET info/external_dbs/:species | --- | --- | | GET info/divisions | get_divisions() | Retrieve Ensembl divisions. | | GET info/genomes/:genome_name | --- | --- | | GET info/genomes/accession/:accession | --- | --- | | GET info/genomes/assembly/:assembly_id | --- | --- | | GET info/genomes/division/:division_name | --- | --- | | GET info/genomes/taxonomy/:taxon_name | --- | --- | | GET info/ping | is_ensembl_reachable() | Check access to the Ensembl REST API server. | | GET info/rest | get_rest_version() | Retrieve the current version of the Ensembl REST API. | | GET info/software | get_software_version() | Retrieve the Perl API version. | | GET info/species | get_species() | Retrieves species-level information. | | GET info/variation/:species | get_variation_sources() | Retrieves variant sources, i.e. a list of databases used by Ensembl for obtaining variant information. | | GET info/variation/consequence_types | get_variant_consequences() | Retrieves variant consequence types. | | GET info/variation/populations/:species:/:population_name | get_individuals() | Retrieves individual-level information. | | GET info/variation/populations/:species | get_populations() | Retrieves population-level information. |

Linkage disequilibrium

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET ld/:species/:id/:population_name | get_ld_variants_by_window() | Gets linkage disequilibrium data by genomic window centred on queried variants. | | GET ld/:species/pairwise/:id1/:id2 | get_ld_variants_by_pair() | Gets linkage disequilibrium data for pairs of queried variants. | | GET ld/:species/region/:region/:population_name | get_ld_variants_by_range() | Gets linkage disequilibrium data by genomic range. |

Lookup

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET lookup/id/:id | --- | --- | | POST lookup/id | --- | --- | | GET lookup/symbol/:species/:symbol | --- | --- | | POST lookup/symbol/:species/:symbol | --- | --- |

Mapping

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET map/cdna/:id/:region | --- | --- | | GET map/cds/:id/:region | --- | --- | | GET map/:species/:asm_one/:region/:asm_two | --- | --- | | GET map/translation/:id/:region | --- | --- |

Ontologies and taxonomy

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET ontology/ancestors/:id | --- | --- | | GET ontology/ancestors/chart/:id | --- | --- | | GET ontology/descendants/:id | --- | --- | | GET ontology/id/:id | --- | --- | | GET ontology/name/:name | --- | --- | | GET taxonomy/classification/:id | --- | --- | | GET taxonomy/id/:id | --- | --- | | GET taxonomy/name/:name | --- | --- |

Overlap

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET overlap/id/:id | --- | --- | | GET overlap/region/:species/:region | --- | --- | | GET overlap/translation/:id | --- | --- |

Phenotype annotations

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET /phenotype/accession/:species/:accession | --- | --- | | GET /phenotype/gene/:species/:gene | --- | --- | | GET /phenotype/region/:species/:region | --- | --- | | GET /phenotype/term/:species/:term | --- | --- |

Regulation

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET regulatory/species/:species/microarray/:microarray/vendor/:vendor | --- | --- | | GET regulatory/species/:species/epigenome | --- | --- | | GET species/:species/binding_matrix/:binding_matrix_stable_id/ | --- | --- | | GET regulatory/species/:species/microarray | --- | --- | | GET regulatory/species/:species/microarray/:microarray/probe/:probe | --- | --- | | GET regulatory/species/:species/microarray/:microarray/probe_set/:probe_set | --- | --- | | GET regulatory/species/:species/id/:id | --- | --- |

Sequence

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET sequence/id/:id | --- | --- | | POST sequence/id | --- | --- | | GET sequence/region/:species/:region | --- | --- | | POST sequence/region/:species | --- | --- |

Transcript haplotypes

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET transcript_haplotypes/:species/:id | --- | --- |

VEP

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET vep/:species/hgvs/:hgvs_notation | --- | --- | | POST vep/:species/hgvs | --- | --- | | GET vep/:species/id/:id | --- | --- | | POST vep/:species/id | --- | --- | | GET vep/:species/region/:region/:allele/ | --- | --- | | POST vep/:species/region | --- | --- |

Variation

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET variant_recoder/:species/:id | --- | --- | | POST variant_recoder/:species | --- | --- | | GET variation/:species/:id | --- | --- | | GET variation/:species/pmcid/:pmcid | --- | --- | | GET variation/:species/pmid/:pmid | --- | --- | | POST variation/:species/ | --- | --- |

Variation GA4GH

| Ensembl REST API | {ensemblr} API | Description | | ---------------- | ---------------- | ----------- | | GET ga4gh/beacon | --- | --- | | GET ga4gh/beacon/query | --- | --- | | POST ga4gh/beacon/query | --- | --- | | GET ga4gh/features/:id | --- | --- | | POST ga4gh/features/search | --- | --- | | POST ga4gh/callsets/search | --- | --- | | GET ga4gh/callsets/:id | --- | --- | | POST ga4gh/datasets/search | --- | --- | | GET ga4gh/datasets/:id | --- | --- | | POST ga4gh/featuresets/search | --- | --- | | GET ga4gh/featuresets/:id | --- | --- | | GET ga4gh/variants/:id | --- | --- | | POST ga4gh/variantannotations/search | --- | --- | | POST ga4gh/variants/search | --- | --- | | POST ga4gh/variantsets/search | --- | --- | | GET ga4gh/variantsets/:id | --- | --- | | POST ga4gh/references/search | --- | --- | | GET ga4gh/references/:id | --- | --- | | POST ga4gh/referencesets/search | --- | --- | | GET ga4gh/referencesets/:id | --- | --- | | POST ga4gh/variantannotationsets/search | --- | --- | | GET ga4gh/variantannotationsets/:id | --- | --- |

ramiromagno/ensemblr documentation built on Oct. 19, 2023, 11:12 a.m.