IGVF background | Knowledge graph of variant function | The rigvf package | Data license | Catalog API | GRanges-based queries | ArangoDB API | Use with Bioconductor | Compute overlap with plyranges | Plot variants with plotgardener | Session info
Package: rigvf 1.5.5
Michael Love
rigvf: R interface to the IGVF Catalog
The IGVF Catalog provides data on the impact of genomic variants on function. The `rigvf` package provides an interface to the IGVF Catalog, allowing easy integration with Bioconductor resources.
Authors:
rigvf_1.5.5.tar.gz
rigvf_1.5.5.zip(r-4.7-any)rigvf_1.5.5.zip(r-4.6-any)rigvf_1.5.5.zip(r-4.5-any)
rigvf_1.5.5.tgz(r-4.6-any)rigvf_1.5.5.tgz(r-4.5-any)
rigvf_1.5.5.tar.gz(r-4.7-any)rigvf_1.5.5.tar.gz(r-4.6-any)
rigvf_1.5.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rigvf/json (API)
| # Install 'rigvf' in R: |
| install.packages('rigvf', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/igvf/rigvf/issues
Pkgdown/docs site:https://igvf.github.io
On BioConductor:rigvf-1.5.3(bioc 3.24)rigvf-1.4.1(bioc 3.23)
thirdpartyclientannotationvariantannotationfunctionalgenomicsgeneregulationgenomicvariationgenetarget
Last updated from:48cf172ad6. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 210 | ||
| linux-devel | OK | 299 | ||
| source / vignettes | OK | 278 | ||
| linux-release | OK | 285 | ||
| macos-release | OK | 206 | ||
| macos-oldrel | OK | 188 | ||
| windows-devel | OK | 404 | ||
| windows-release | OK | 421 | ||
| windows-oldrel | OK | 413 | ||
| wasm-release | OK | 168 |
Exports:db_edgesdb_gene_elementsdb_gene_variantsdb_nodeselement_geneselementsgene_elementsgene_variantsportal_filesvariant_genes
Dependencies:askpassBiocGenericscachemclicpp11curldplyrfastmapgenericsGenomicRangesgluehttr2IRangesjsonlitelifecyclemagrittrmemoiseopensslpillarpkgconfigpurrrR6rjsonconsrlangS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswhiskerwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Internal interface to ArangoDB REST API | arango arango_auth arango_collections arango_cursor arango_request |
| Query the IGVF Catalog via REST API | catalog_queries elements element_genes gene_elements gene_variants variant_genes |
| Query the IGVF Catalog via ArangoDB | db_edges db_gene_elements db_gene_variants db_nodes db_queries |
| Query the IGVF Data Portal | portal_files portal_queries |
| Package configuration global variable management | rigvf rigvf_config |