AnVILVRS | Introduction | Installation | Loading and Setup | Usage | Translating Variant Identifiers | Allele Object Retrieval | Variant Retrieval from Allele Object | Calculating Cohort Allele Frequency | Population Descriptor table download | SeqRepo reference data | Cohort Allele Frequency (CAF) calculation | Session Info
Package: AnVILVRS 0.99.19
Marcel Ramos
AnVILVRS: Expose the vrs_anvil_toolkit Python package via R
Process Variant Call Format (VCF) files and perform lookup operations on Genomic Variation Representation Service (GA4GH VRS) identifiers. The GA4GH VRS identifiers provide a standardized way to represent genomic variations, making it easier to exchange and share genomic information.
Authors:
AnVILVRS_0.99.19.tar.gz
AnVILVRS_0.99.19.zip(r-4.7)AnVILVRS_0.99.19.zip(r-4.6)AnVILVRS_0.99.19.zip(r-4.5)
AnVILVRS_0.99.19.tgz(r-4.6-any)AnVILVRS_0.99.19.tgz(r-4.5-any)
AnVILVRS_0.99.19.tar.gz(r-4.7-any)AnVILVRS_0.99.19.tar.gz(r-4.6-any)
AnVILVRS_0.99.19.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AnVILVRS/json (API)
| # Install 'AnVILVRS' in R: |
| install.packages('AnVILVRS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/anvilvrs/issues
On BioConductor:AnVILVRS-0.99.19(bioc 3.24)
softwarebiologicalquestionvariantannotationinfrastructurethirdpartyclientu24hg010263
Last updated from:70f940eb2c. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 171 | ||
| linux-devel-x86_64 | OK | 265 | ||
| source / vignettes | OK | 262 | ||
| linux-release-x86_64 | OK | 219 | ||
| macos-release-arm64 | OK | 126 | ||
| macos-oldrel-arm64 | OK | 96 | ||
| windows-devel | OK | 108 | ||
| windows-release | OK | 104 | ||
| windows-oldrel | OK | 116 | ||
| wasm-release | OK | 123 |
Exports:build_vrs_indexget_cafget_pop_descriptorget_seqrepoget_variant_from_alleleget_vrs_alleleget_vrs_idinstall_AnVILVRSsetup_vrs_toolkit
Dependencies:AnVILBaseAnVILGCPaskpassBiocBaseUtilsBiocFileCachebitbit64blobcachemclicpp11curlDBIdbplyrdplyrfastmapfilelockGCPtoolsgenericsglueherehttrhttr2jsonlitelatticelifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsRcppRcppTOMLreticulaterlangrprojrootRSQLitestringistringrsystibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Generate a VRS-VCF index database | build_vrs_index |
| Get the allele frequency from 1000 Genomes Project VCF file | get_caf |
| Downloads the population descriptor file to the BiocFileCache from a known Google Storage URI. | get_pop_descriptor |
| Run rsync on SeqRepo snapshot | get_seqrepo |
| Translate a Variant to a VRS ID | get_variant_from_allele get_vrs_allele get_vrs_id |
| Install AnVILVRS Python Environment | install_AnVILVRS |
| Set up the VRS AnVIL Toolkit repository | setup_vrs_toolkit |
