Package: GA4GHclient 1.29.0

Welliton Souza

GA4GHclient: A Bioconductor package for accessing GA4GH API data servers

GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.

Authors:Welliton Souza [aut, cre], Benilton Carvalho [ctb], Cristiane Rocha [ctb]

GA4GHclient_1.29.0.tar.gz
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GA4GHclient.pdf |GA4GHclient.html✨
GA4GHclient/json (API)
NEWS

# Install 'GA4GHclient' in R:

install.packages('GA4GHclient', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/labbcb/ga4ghclient/issues

On BioConductor:GA4GHclient-1.29.0(bioc 3.20)GA4GHclient-1.28.0(bioc 3.19)

bioconductor-package

39 exports 1.00 score 79 dependencies 1 dependents

Last updated 2 months agofrom:9d635c1789

Exports:getBiosample getCallSet getDataset getExpressionLevel getFeature getFeatureSet getIndividual getReadGroupSet getReference getReferenceSet getRnaQuantification getRnaQuantificationSet getVariant getVariantAnnotationSet getVariantSet HGVSnames listReferenceBases makeVCFFromGA4GHResponse makeVCFHeaderFromGA4GHResponse searchBiosamples searchCallSets searchDatasets searchExpressionLevels searchFeatures searchFeatureSets searchIndividuals searchPhenotypeAssociations searchPhenotypeAssociationSets searchReadGroupSets searchReads searchReferences searchReferenceSets searchRnaQuantifications searchRnaQuantificationSets searchVariantAnnotations searchVariantAnnotationSets searchVariants searchVariantsByGRanges searchVariantSets

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI DelayedArray dplyr fansi fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 VariantAnnotation vctrs withr XML XVector yaml zlibbioc

GA4GHclient

Welliton Souza

Rendered fromGA4GHclient.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2017-10-11
Started: 2017-03-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A Bioconductor package for accessing GA4GH API data server	GA4GHclient-package GA4GHclient
getBiosample function	getBiosample
getCallSet function	getCallSet
getDataset function	getDataset
getExpressionLevel function	getExpressionLevel
getFeature function	getFeature
getFeatureSet function	getFeatureSet
getIndividual function	getIndividual
getReadGroupSet function	getReadGroupSet
getReference function	getReference
getReferenceSet function	getReferenceSet
getRnaQuantification function	getRnaQuantification
getRnaQuantificationSet function	getRnaQuantificationSet
getVariant function	getVariant
Gets getVariantAnnotationSet function	getVariantAnnotationSet
getVariantSet function.	getVariantSet
Generate genomic variant data to HGVS nomenclature	HGVSnames
listReferenceBases function	listReferenceBases
makeVCFFromGA4GHResponse function	makeVCFFromGA4GHResponse
makeVCFHeaderFromGA4GHResponse function	makeVCFHeaderFromGA4GHResponse
searchBiosamples function	searchBiosamples
searchCallSets function	searchCallSets
searchDatasets function	searchDatasets
searchExpressionLevels function	searchExpressionLevels
searchFeatures function	searchFeatures
searchFeatureSets function	searchFeatureSets
searchIndividuals function	searchIndividuals
searchPhenotypeAssociations function	searchPhenotypeAssociations
searchPhenotypeAssociationSets function	searchPhenotypeAssociationSets
searchReadGroupSets function	searchReadGroupSets
searchReads function	searchReads
searchReferences function	searchReferences
searchReferenceSets function	searchReferenceSets
searchRnaQuantifications function	searchRnaQuantifications
searchRnaQuantificationSets function	searchRnaQuantificationSets
searchVariantAnnotations function	searchVariantAnnotations
searchVariantAnnotationSets function	searchVariantAnnotationSets
searchVariants function	searchVariants
searchVariantsByGranges function	searchVariantsByGRanges
searchVariantSets function	searchVariantSets