Package: Rduckvep 0.1.0

Sounkou Mahamane Toure

Rduckvep: DuckDB Variant Consequence Annotation

Builds and loads the bundled DuckVEP C extension for relation-first variant consequence and phased-haplotype annotation.

Authors:Sounkou Mahamane Toure [aut, cre]

Rduckvep_0.1.0.tar.gz
Rduckvep_0.1.0.zip(r-4.7-any)Rduckvep_0.1.0.zip(r-4.6-any)Rduckvep_0.1.0.zip(r-4.5-any)
Rduckvep_0.1.0.tgz(r-4.6-any)Rduckvep_0.1.0.tgz(r-4.5-any)
Rduckvep_0.1.0.tar.gz(r-4.7-any)Rduckvep_0.1.0.tar.gz(r-4.6-any)
Rduckvep_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rduckvep/json (API)

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

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

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

On CRAN:

Conda:

3.23 score 2 stars 21 exports 2 dependencies

Last updated from:d82ad2bd26. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK143
source / vignettesOK202
linux-releaseOK147
macos-releaseOK166
macos-oldrelOK181
windows-develOK127
windows-releaseOK186
windows-oldrelOK159
wasm-releaseOK118

Exports:rduckvep_annotaterduckvep_annotate_sqlrduckvep_coding_callsrduckvep_coding_transcriptsrduckvep_connectrduckvep_ensembl_regions_sqlrduckvep_ensembl_regulation_features_sqlrduckvep_ensembl_transcripts_sqlrduckvep_haplotypesrduckvep_loadrduckvep_load_modelrduckvep_lof_sqlrduckvep_model_receipt_sqlrduckvep_prepare_breakend_fusionrduckvep_prepare_breakend_pairsrduckvep_prepare_expansionhunterrduckvep_prepare_structural_hgvsrduckvep_prepare_sv_geometryrduckvep_restore_modelrduckvep_save_modelrduckvep_transcript_projection_sql

Dependencies:DBIduckdb

Readme and manuals

Help Manual

Help pageTopics
Annotate events using a loaded DuckVEP modelrduckvep_annotate
Generate DuckVEP SQL on the caller's connectionrduckvep_annotate_sql rduckvep_builders rduckvep_ensembl_regions_sql rduckvep_ensembl_regulation_features_sql rduckvep_ensembl_transcripts_sql rduckvep_lof_sql rduckvep_model_receipt_sql rduckvep_transcript_projection_sql
Read the Coding Calls of a VCF or BCF Filerduckvep_coding_calls
Find the Transcripts Whose Coding Sequence Events Overlaprduckvep_coding_transcripts
Open DuckDB with DuckVEP loadedrduckvep_connect
Replay Phased Transcript Haplotypesrduckvep_haplotypes
Load the bundled DuckVEP extensionrduckvep_load
Load a resident transcript model, on either DuckDB C API hostrduckvep_load_model
Combine BND identity with endpoint genesrduckvep_prepare_breakend_fusion
Validate BND mate and event identityrduckvep_prepare_breakend_pairs
Prepare ExpansionHunter v5 repeat allelesrduckvep_prepare_expansionhunter
Prepare structural HGVS descriptionsrduckvep_prepare_structural_hgvs
Prepare VCF structural geometry and insertion provenancerduckvep_prepare_sv_geometry
Save and restore a resident model as a snapshot filerduckvep_restore_model rduckvep_save_model