Package: AnnotationHubData 1.43.0

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]

AnnotationHubData_1.43.0.tar.gz
AnnotationHubData_1.43.0.zip(r-4.7)AnnotationHubData_1.43.0.zip(r-4.6)AnnotationHubData_1.43.0.zip(r-4.5)

AnnotationHubData_1.43.0.tar.gz(r-4.7-any)AnnotationHubData_1.43.0.tar.gz(r-4.6-any)
AnnotationHubData_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AnnotationHubData/json (API)

# Install 'AnnotationHubData' in R:

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

On BioConductor:AnnotationHubData-1.43.0(bioc 3.24)AnnotationHubData-1.42.0(bioc 3.23)

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

dataimport

4.92 score 3 packages 23 scripts 46 exports 108 dependencies

Last updated from:47cd0eec3f. Checks:1 ERROR, 5 WARNING, 2 OK, 2 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	217
linux-devel-x86_64	WARNING	569
source / vignettes	OK	301
linux-release-x86_64	WARNING	592
macos-release-arm64	FAIL	3773
macos-oldrel-arm64	FAIL	3706
windows-devel	WARNING	674
windows-release	WARNING	543
windows-oldrel	WARNING	633
wasm-release	OK	176

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 Biostrings bit bit64 bitops blob cachem callr cigarillo cli codetools commonmark cpp11 crayon curl DBI dbplyr DelayedArray dplyr evaluate fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue graph highr httr httr2 IRanges jsonlite KEGGREST knitr lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl OrganismDbi otel pillar pkgconfig png processx ps purrr R6 rappdirs RBGL RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer RUnit rvest S4Arrays S4Vectors selectr Seqinfo snow SparseArray stringdist stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr xfun XML xml2 XVector yaml

Introduction to AnnotationHubData

Overview | Creating an AnnotationHub Package or Converting to an AnnotationHub Package | Historical vignettes

Rendered fromIntroductionToAnnotationHubData.Rmdusingknitr::rmarkdown

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