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 1.5.0
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_1.5.0.tar.gz
rigvf_1.5.0.zip(r-4.7)rigvf_1.5.0.zip(r-4.6)rigvf_1.5.0.zip(r-4.5)
rigvf_1.5.0.tgz(r-4.6-any)rigvf_1.5.0.tgz(r-4.5-any)
rigvf_1.5.0.tar.gz(r-4.7-any)rigvf_1.5.0.tar.gz(r-4.6-any)
rigvf_1.5.0.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-1.5.0(bioc 3.24)rigvf-1.4.0(bioc 3.23)
thirdpartyclientannotationvariantannotationfunctionalgenomicsgeneregulationgenomicvariationgenetarget
Last updated from:6e322af6d3. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 262 | ||
| linux-devel-x86_64 | OK | 345 | ||
| source / vignettes | OK | 313 | ||
| linux-release-x86_64 | OK | 345 | ||
| macos-release-arm64 | OK | 157 | ||
| macos-oldrel-arm64 | OK | 185 | ||
| windows-devel | OK | 411 | ||
| windows-release | OK | 408 | ||
| windows-oldrel | OK | 433 | ||
| wasm-release | OK | 231 |
Exports:db_edgesdb_gene_elementsdb_gene_variantsdb_nodeselement_geneselementsgene_elementsgene_variantsvariant_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 |
| Package configuration global variable management | rigvf rigvf_config |
