Look up genes, variants and proteins from R. One consistent way to call gnomAD, ClinVar, UniProt, Ensembl and the other databases you already use, instead of writing a client for each one.
Documentation is at https://www.samuelbharti.com/bioclients/.
install.packages("bioclients")For the development version:
pak::pak("samuelbharti/bioclients/pkg-r")r-universe builds from main and serves prebuilt binaries, so it has fixes
before they reach CRAN:
install.packages("bioclients", repos = "https://samuelbharti.r-universe.dev")library(bioclients)
res <- mygene_gene("TP53")
res$status
#> [1] "ok"
biohttp::body_or_null(res)
#> # A tibble: 1 x 8
#> symbol name summary entrez ensembl_gene uniprot hgnc type_of_gene
#> TP53 tumor protein p53 This g. 7157 ENSG00000141510 P04637 11998 protein-cod.Every client returns an envelope rather than raising, so you branch on
res$status and write no tryCatch() of your own. A source that has nothing to
say answers no_data, which is an answer rather than a fault.
Ask about many genes at once and the answer comes back one row per input, in the order you asked:
res <- mygene_genes(c("TP53", "NOT_A_GENE", "BRAF"))
biohttp::body_or_null(res)
#> # A tibble: 3 x 8
#> symbol entrez ...
#> TP53 7157
#> NOT_A_GENE NA <- a row of NA, not a dropped row
#> BRAF 673A miss keeps its row, because a shorter table silently shifts every row after it onto the wrong gene.
The same clients keep getting written across the app family, and the copies
drift in ways that are hard to see from inside any one app. This package is the
one copy, laid out the way genescout already lays them out: one file per
service, with the client kept separate from the parser.
bioclients fetches and parses, and stops there. Ranking, scoring, curation and
disease-to-gene assembly belong to the app that calls it. Retries, caching and
error handling belong to biohttp
underneath. There is no Shiny code here.
Each service below has a client. The tables group them by what you are looking up rather than alphabetically.
| Service | Single call | Batch call | Parser |
|---|---|---|---|
| MyGene | mygene_gene() |
mygene_genes() |
mygene_parse_hits(), mygene_parse_batch() |
Nearly every other lookup starts here, because the rest are keyed on an Entrez, Ensembl, UniProt or HGNC id rather than a symbol.
| Service | Single call | Batch call | Parser |
|---|---|---|---|
| gnomAD constraint | gnomad_constraint() |
gnomad_constraints() |
gnomad_parse_constraint(), gnomad_parse_constraints() |
| gnomAD frequency | gnomad_frequency(), gnomad_frequency_by_id() |
gnomad_frequencies() |
gnomad_parse_frequency(), gnomad_parse_variant(), gnomad_parse_variants(), gnomad_parse_populations() |
| ClinVar | clinvar_classification() |
clinvar_parse_record(), clinvar_category() |
|
| MyVariant | myvariant_variants() |
myvariant_parse_record(), myvariant_parse_batch() |
|
| Ensembl VEP | vep_variants(), vep_variants_all() |
vep_parse_element(), vep_parse_colocated(), vep_parse_batch() |
|
| Ensembl REST | ensembl_vep_id(), ensembl_gene_model() |
ensembl_parse_vep(), ensembl_parse_gene_model() |
|
| VariantValidator | variantvalidator_normalize() |
variantvalidator_parse() |
|
| ClinGen Allele Registry | clingen_alleles() |
clingen_parse_allele(), clingen_parse_batch() |
| Service | Single call | Batch call | Parser |
|---|---|---|---|
| Open Targets | opentargets_gene_diseases(), opentargets_disease_targets(), opentargets_resolve_disease(), opentargets_drugs(), opentargets_pgx() |
opentargets_parse_diseases(), opentargets_parse_targets(), opentargets_parse_matches() |
|
| DGIdb | dgidb_gene() |
dgidb_genes() |
dgidb_parse_genes() |
| Pharos | pharos_target() |
pharos_targets() |
pharos_parse_targets() |
| CIViC | civic_gene() |
civic_parse_gene() |
|
| JensenLab DISEASES | diseases_channel(), diseases_gene_associations() |
diseases_parse_channel(), diseases_merge_channels() |
|
| PanelApp | panelapp_panel(), panelapp_panels() |
panelapp_all_panels() |
panelapp_parse_index(), panelapp_parse_panel() |
| ClinGen gene validity | clingen_validity_for() |
clingen_gene_validity() |
clingen_parse_validity() |
| Service | Single call | Batch call | Parser |
|---|---|---|---|
| UniProt | uniprot_diseases(), uniprot_features() |
uniprot_parse_diseases(), uniprot_parse_features() |
|
| ProtVar | protvar_function(), protvar_population() |
protvar_parse_function(), protvar_parse_population() |
|
| AlphaFold | alphafold_model() |
alphafold_parse_model() |
|
| PDBe | pdbe_structures() |
pdbe_parse_structures() |
|
| STRING | string_partners(), string_network() |
string_map_ids() |
string_parse_partners(), string_parse_network() |
| Service | Single call | Batch call | Parser |
|---|---|---|---|
| GTEx | gtex_median_expression(), gtex_gene_reference() |
gtex_parse_expression(), gtex_parse_reference() |
|
| Human Protein Atlas | hpa_gene() |
hpa_parse_gene() |
|
| QuickGO | quickgo_annotations() |
quickgo_parse_annotations() |
|
| Reactome | reactome_pathways() |
reactome_parse_pathways() |
| Service | Single call | Batch call | Parser |
|---|---|---|---|
| HPO | hpo_search(), hpo_term(), hpo_gene_annotation() |
hpo_parse_search(), hpo_parse_term(), hpo_parse_diseases() |
|
| Monarch | monarch_search(), monarch_associations(), monarch_gene_phenotypes() |
monarch_parse_search(), monarch_parse_associations() |
|
| IMPC | impc_mouse_ortholog(), impc_gene_phenotypes() |
impc_parse_ortholog(), impc_parse_phenotypes() |
| Service | Single call | Batch call | Parser |
|---|---|---|---|
| Europe PMC | europepmc_search(), europepmc_count() |
europepmc_parse_results(), europepmc_parse_count() |
|
| PubTator3 | pubtator_gene_literature() |
pubtator_parse_results(), pubtator_parse_count() |
pkg-r/_pkgdown.yml holds the same grouping for the reference index, and
NEWS.md lists the verified behaviour each client pins.
The package is archived on Zenodo. Use the concept DOI, which always resolves to the newest archived release:
Bharti, S. (2026). bioclients: Clients for Biological Database Web Services. Zenodo. https://doi.org/10.5281/zenodo.21770870
CITATION.cff carries the same metadata and one identifier per archived
version, so citation("bioclients") in R and the "Cite this repository" button
on GitHub both work.
Barret Schloerke and Carson Sievert advise this work as thesis advisors. Posit Software, PBC funded early work on this package and holds copyright together with the author.
MIT. See LICENSE.