Package: AnnotationHubData 1.35.0

Bioconductor Package Maintainer

AnnotationHubData: Transform public data resources into Bioconductor Data Structures

These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

Authors:Martin Morgan [ctb], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb], Paul Shannon [ctb], Lori Shepherd [ctb], Bioconductor Package Maintainer [cre]

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AnnotationHubData.pdf |AnnotationHubData.html✨
AnnotationHubData/json (API)
NEWS

# Install 'AnnotationHubData' in R:

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

On BioConductor:AnnotationHubData-1.35.0(bioc 3.20)AnnotationHubData-1.34.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

46 exports 2.09 score 114 dependencies 3 dependents

Last updated 2 months agofrom:056e918702

Exports:ahmToJson AnnotationHubMetadata annotationHubRoot checkSpeciesTaxId constructSeqInfo deleteResources ensemblFastaToFaFile ensemblFastaToTwoBitFile flog gencodeFastaToFaFile getImportPreparerClasses getSpeciesList getValidSourceTypes hubError hubError<-HubMetadataFromJson inputFiles makeAnnotationHubMetadata makeAnnotationHubResource makeEnsemblFastaToAHM makeEnsemblTwoBitToAHM makeGencodeFastaToAHM makeNCBIToOrgDbsToAHM makeStandardOrgDbsToAHM makeStandardTxDbsToAHM metadata metadata<-metadataList metadataTable newResources outputFile pushMetadata pushResources recipeName run runRecipes show sourceUrls suggestSpecies toJson UCSCTrackImportPreparer updateResources upload_to_azure upload_to_S3 validDispatchClass validSpecies

Dependencies:abind AnnotationDbi AnnotationForge AnnotationHub askpass BH Biobase BiocBaseUtils BiocCheck BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biocViews biomaRt Biostrings bit bit64 bitops blob cachem callr cli codetools cpp11 crayon curl DBI dbplyr DelayedArray digest dplyr evaluate fansi fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue graph highr hms httr httr2 IRanges jsonlite KEGGREST knitr lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl OrganismDbi pillar pkgconfig plogr png prettyunits processx progress ps purrr R6 rappdirs RBGL RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer RUnit rvest S4Arrays S4Vectors selectr snow SparseArray stringdist stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker UCSC.utils utf8 vctrs withr xfun XML xml2 XVector yaml zlibbioc

Introduction to AnnotationHubData

Lori Shepherd

Rendered fromIntroductionToAnnotationHubData.Rmdusingknitr::rmarkdownon Jun 16 2024.

Last update: 2021-09-10
Started: 2016-08-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Transform public data resources into Bioconductor Data Structures	AnnotationHubData-package AnnotationHubRecipes
Class '"AnnotationHubMetadata"' and methods	ahmToJson AnnotationHubMetadata AnnotationHubMetadata-class class:AnnotationHubMetadata class:HubMetadata constructSeqInfo deleteResources getImportPreparerClasses hubError hubError,HubMetadata-method hubError,list-method hubError<- hubError<-,HubMetadata,character-method hubError<-,list,character-method HubMetadata HubMetadata-class HubMetadataFromJson inputFiles inputFiles,HubMetadata-method makeAnnotationHubResource metadata metadata,HubMetadata-method metadata<- metadata<-,HubMetadata,list-method outputFile outputFile,HubMetadata-method recipeName recipeName,HubMetadata-method run run,AnnotationHubMetadata-method show show,HubMetadata-method toJson
flog	flog
Class 'ImportPreparer' and generic 'newResources'	annotationHubRoot dbSNPVCFImportPreparer dbSNPVCFImportPreparer-class EncodeImportPreparer EncodeImportPreparer-class EnsemblFastaImportPreparer EnsemblFastaImportPreparer-class EnsemblGtfImportPreparer EnsemblGtfImportPreparer-class getImportPreparer Grasp2ImportPreparer Grasp2ImportPreparer-class HaemCodeImportPreparer HaemCodeImportPreparer-class ImportPreparer-class Inparanoid8ImportPreparer Inparanoid8ImportPreparer-class metadataList metadataTable NCBIImportPreparer NCBIImportPreparer-class newResources newResources,dbSNPVCFImportPreparer-method newResources,EncodeImportPreparer-method newResources,EnsemblFastaImportPreparer-method newResources,EnsemblGtfImportPreparer-method newResources,Grasp2ImportPreparer-method newResources,HaemCodeImportPreparer-method newResources,ImportPreparer-method newResources,Inparanoid8ImportPreparer-method newResources,NCBIImportPreparer-method newResources,RefNetImportPreparer-method newResources,UCSCChainPreparer-method newResources,UCSCFullTrackImportPreparer-method newResources,UCSCTrackImportPreparer-method RefNetImportPreparer RefNetImportPreparer-class show,ImportPreparer-method sourceUrls UCSCChainPreparer UCSCChainPreparer-class UCSCTrackImportPreparer UCSCTrackImportPreparer-class
Make AnnotationHubMetadata objects from csv file of metadata	makeAnnotationHubMetadata
Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.	ensemblFastaToFaFile ensemblFastaToTwoBitFile makeEnsemblFasta makeEnsemblFastaToAHM makeEnsemblTwoBitToAHM
Recipe to add Gencode FASTA resources to AnnotationHub	gencodeFastaToFaFile makeGencodeFasta makeGencodeFastaToAHM
Functions to add OrgDb and TxDb sqlite files to AnnotationHub	makeNCBIToOrgDbsToAHM makeNonStandardOrgDbs makeStandardOrgDbs makeStandardOrgDbsToAHM makeStandardTxDbs makeStandardTxDbsToAHM
updateResources	pushMetadata pushResources runRecipes runRecipes,AnnotationHubMetadata-method updateResources
Upload a file to Microsoft Azure Data Lake	Azure AZURE_SAS_URL DataLake upload_to_azure
Upload a file to Amazon S3	amazon AWS S3 upload_to_S3
ValidationFunctions	checkSpeciesTaxId getSpeciesList getValidSourceTypes suggestSpecies validationFunctions validDispatchClass validSpecies