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rentrez - 'Entrez' in R

Provides an R interface to the NCBI's 'EUtils' API, allowing users to search databases like 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and 'PubMed' <https://pubmed.ncbi.nlm.nih.gov/>, process the results of those searches and pull data into their R sessions.

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15.31 score 221 stars 129 dependents 1.3k scripts 50k downloads

biohttp - Normalized HTTP Transport with Circuit Breaking and Caching

Web service calls return a normalized result value instead of raising a condition, so a caller branches on data rather than on an error handler. Transport failure, a non-success status code, and an unreadable response body are reported as three distinct outcomes. Per-host circuit breaking, retry with a transient-failure predicate, optional throttling, redacted request headers, and a success-only cache come as defaults. Many questions to one source can be asked as a single batch, where only the entries the cache is missing reach the network. Service-specific knowledge is left to the client packages built on top. The circuit breaker is the pattern described in Nygard (2018, ISBN:9781680502398).

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api-clientbioinformaticscachingcircuit-breakerhttphttr2retry

4.95 score 2 stars 1 dependents 6 scripts 323 downloads

biocohort - Cohort Objects for Subjects and Samples in Omics Studies

Keeps the subjects, samples, and analysis outputs of a study in one validated object. It starts from a sample manifest with one row per sample, which is read, checked, and split into a subject table and a sample map. Species and assay are plain values in those tables rather than fixed types, so the same object serves any organism and any omics assay. From that object the package writes the sample sheet a pipeline expects, pairs tumor and normal samples on demand, and records where each analysis writes its output so the files can be loaded back in by subject or by pair. Manual corrections are kept in an audit trail. Results can also be translated across genome builds or species, with liftover for coordinates and ortholog mapping for genes.

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4.35 score 3 stars 5 scripts 377 downloads

biobouncer - Validate Biological Identifiers and Inputs

Gene symbols, ontology terms, variant formats, and database accessions are validated through one small application programming interface (API), either offline against identifier patterns and bundled snapshots or live against a source web service. Results are designed to match those of the companion 'Python' and 'JavaScript' packages for the same inputs. Input order and length are preserved, and errors are reported explicitly rather than as a silent failure. Identifier patterns follow the registry and nomenclature described in Hoyt et al. (2022) <doi:10.1038/s41597-022-01807-3> and den Dunnen et al. (2016) <doi:10.1002/humu.22981>.

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bioinformaticsdatabase-toolsjspythonshinyvalidate

4.28 score 4 stars 12 scripts 244 downloads

plotomics - High-Performance Bioinformatics Visualizations

Lightweight, GPU-accelerated bioinformatics visualization widgets (volcano plots, expression and clustered heatmaps, dot plots, stacked violins, embeddings, spatial tissue maps, oncoprints, protein domain lollipops, Kaplan-Meier curves, mutational signature profiles, UpSet plots, treemaps, networks and Hi-C contact matrices) backed by a shared JavaScript core and exposed to R through 'htmlwidgets'. Designed for large datasets that render smoothly in the browser, the 'RStudio' Viewer, R Markdown, Quarto and Shiny.

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anywidgetbioinformaticsdata-visualizationgenomicsheatmaphtmlwidgetsjupyteroncoprintpythonshinysingle-celltypescriptvisualizationwebgl

4.02 score 3 stars 8 scripts 299 downloads

peacock - Quick Project Initialization with Templates

Initialize project directory structures from pre-configured templates. Scaffolds for 'Shiny' applications, reproducible analyses, 'Quarto' projects, 'Python' projects, and tool comparisons are created with one function call. Arbitrary 'GitHub' repositories can also serve as templates via a built-in registry.

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boilerplateinitializationtemplateworkflow

3.90 score 4 stars 5 scripts

bioclients - Clients for Biological Database Web Services

Look up genes, variants and proteins from R, without writing a client for every biological web service. Each service gets one client that makes the request and returns a table. Parsing is a separate function that needs no network, so it can run on a saved response and be tested offline. Transport, retries, caching and error handling are left to the 'biohttp' package. Dependencies for single services are optional, so you do not install what you will not use. The services covered include 'Ensembl', described in Dyer et al. (2025) <doi:10.1093/nar/gkae1071>, 'UniProt', in The UniProt Consortium (2025) <doi:10.1093/nar/gkae1010>, 'gnomAD', in Chen et al. (2024) <doi:10.1038/s41586-023-06045-0>, 'Open Targets', in Buniello et al. (2025) <doi:10.1093/nar/gkae1128>, and the 'AlphaFold' Protein Structure Database, in Varadi et al. (2024) <doi:10.1093/nar/gkad1011>. Each client's help page cites the service it calls.

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api-clientbioinformaticsgene-annotationgenomicshttr2variant-annotationweb-services

2.78 score 2 stars 8 scripts 381 downloads