Package: RClinVarbitration 0.1.1

Sounkou Mahamane Toure

RClinVarbitration: Stream ClinVar XML into Relational DuckDB Tables

Streams official 'ClinVar' VCV XML releases, including gzip inputs, into focused relational tables in 'DuckDB'. A package-owned native extension uses libxml2's forward reader to retain VCV variants, normalized alleles, RCV aggregates, SCV submissions, conditions, observations, citations, and attributable evidence text without loading the release into R. ClinVarbitration policy is a derived SQL layer over those retained source relations, with a separate direct reproducer for archived NCBI flat-file releases.

Authors:Sounkou Mahamane Toure [aut, cre], DuckDB Foundation [cph], Centre for Population Genomics [cph]

RClinVarbitration_0.1.1.tar.gz
RClinVarbitration_0.1.1.zip(r-4.7)RClinVarbitration_0.1.1.zip(r-4.6)RClinVarbitration_0.1.1.zip(r-4.5)
RClinVarbitration_0.1.1.tgz(r-4.6-any)RClinVarbitration_0.1.1.tgz(r-4.5-any)
RClinVarbitration_0.1.1.tar.gz(r-4.7-any)RClinVarbitration_0.1.1.tar.gz(r-4.6-any)
RClinVarbitration_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RClinVarbitration/json (API)

# Install 'RClinVarbitration' in R:
install.packages('RClinVarbitration', repos = c('https://rgenomicsetl.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rgenomicsetl/rclinvarbitration/issues

Pkgdown/docs site:https://rgenomicsetl.github.io

On CRAN:

Conda:

bioinformaticsclinvarduckdbgenomics

3.18 score 10 exports 1 dependencies

Last updated from:1700ec9a53. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK208
source / vignettesOK223
linux-release-x86_64OK148
macos-release-arm64OK108
macos-oldrel-arm64OK93
windows-develOK103
windows-releaseOK116
windows-oldrelOK99
wasm-releaseOK114

Exports:rclinvarbitration_download_clinvarrclinvarbitration_enablerclinvarbitration_export_clinvarbitration_parquetrclinvarbitration_extension_pathrclinvarbitration_import_xmlrclinvarbitration_initrclinvarbitration_policy_sqlrclinvarbitration_policy_versionrclinvarbitration_reproduce_clinvarbitration_parquetrclinvarbitration_schema_sql

Dependencies:DBI

ClinVarbitration arbitration algorithm
Scope and authority | Inputs retained for arbitration | Step 1: classification bins | Step 2: exclusions | Step 3: SCV version deduplication | Step 4: 2016 evidence window | Step 5: decisive strong review | Step 6: 60/20 arbitration | Step 7: star assignment | Disease identity | Output and audit columns | Complete-release differential validation
Rendered fromarbitration-algorithm.Rmdusingknitr::rmarkdown

Last update: 2026-07-21
Started: 2026-07-21

Semantic retrieval, DuckLake, and VariantStory
Motivation beyond variant annotation | Discovery-oriented views | Using ducksemantics | Publishing releases to DuckLake | VariantStory boundary | Talos 11.1 compatibility target
Rendered fromsemantic-ducklake-variantstory.Rmdusingknitr::rmarkdown

Last update: 2026-07-21
Started: 2026-07-21

Storage, caching, and full-release performance
What is cached? | Download cache | Exact DuckDB extension artifacts | Persistent relational release store | Import lifecycle | What remains virtual? | Measured complete-release conversion
Rendered fromstorage-cache-and-performance.Rmdusingknitr::rmarkdown

Last update: 2026-07-21
Started: 2026-07-21

Readme and manuals

Help Manual

Help pageTopics
Download official ClinVar source filesrclinvarbitration_download_clinvar
Enable native ClinVar XML scanning on a DuckDB connectionrclinvarbitration_enable
Export an allele-level ClinVarbitration-compatible Parquet filerclinvarbitration_export_clinvarbitration_parquet
Locate a version-matched RClinVarbitration DuckDB extensionrclinvarbitration_extension_path
Stream a ClinVar VCV XML release into relational DuckDB tablesrclinvarbitration_import_xml
Initialize the ClinVar relational schemarclinvarbitration_init
ClinVarbitration policy SQLrclinvarbitration_policy_sql
Current ClinVarbitration policy versionrclinvarbitration_policy_version
Reproduce ClinVarbitration decisions from archived ClinVar flat filesrclinvarbitration_reproduce_clinvarbitration_parquet
ClinVar relational schema SQLrclinvarbitration_schema_sql