recipe bioconductor-annotationhub

Client to access AnnotationHub resources

Homepage

https://bioconductor.org/packages/3.12/bioc/html/AnnotationHub.html

License

Artistic-2.0

Recipe

/bioconductor-annotationhub/meta.yaml

Links

biotools: annotationhub, doi: 10.1038/nmeth.3252

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

package bioconductor-annotationhub

Versions

2.22.0-0,  2.20.0-0,  2.18.0-0,  2.16.0-1,  2.14.5-0,  2.14.2-0,  2.12.1-0,  2.10.1-0,  2.10.0-0, 

2.22.0-0,  2.20.0-0,  2.18.0-0,  2.16.0-1,  2.14.5-0,  2.14.2-0,  2.12.1-0,  2.10.1-0,  2.10.0-0,  2.8.2-0,  2.6.0-0

Depends

• bioconductor-annotationdbi >=1.52.0,<1.53.0

• bioconductor-biocfilecache >=1.14.0,<1.15.0

• bioconductor-biocgenerics >=0.36.0,<0.37.0

• bioconductor-biocversion >=3.12.0,<3.13.0

• bioconductor-interactivedisplaybase >=1.28.0,<1.29.0

• bioconductor-s4vectors >=0.28.0,<0.29.0

• r-base >=4.0,<4.1.0a0

• r-biocmanager

• r-curl

• r-dplyr

• r-httr

• r-rappdirs

• r-rsqlite

• r-yaml

Required By

• bioconductor-metagxbreast

• bioconductor-tximeta

• bioconductor-experimenthub

• bioconductor-tenxpbmcdata

• bioconductor-metagxovarian

• bioconductor-scmeth

• r-acidgenomes

• bioconductor-genomicscores

• bioconductor-droplettestfiles

• bioconductor-depmap

• bioconductor-encodexplorer

• bioconductor-customcmpdb

• bioconductor-nestlink

• bioconductor-alpinedata

• bioconductor-annotationhubdata

• bioconductor-org.mxanthus.db

• bioconductor-regutools

• bioconductor-ularcirc

• bioconductor-adductdata

• bioconductor-alternativesplicingevents.hg19

• bioconductor-scrnaseq

• bioconductor-proteomicsannotationhubdata

• bioconductor-hmp2data

• bioconductor-spatiallibd

• bioconductor-fieldeffectcrc

• bioconductor-panther.db

• bioconductor-annotatr

• bioconductor-epitxdb.hs.hg38

• bioconductor-sesamedata

• bioconductor-restfulse

• bioconductor-msnid

• bioconductor-hipathia

• bioconductor-enmix

• bioconductor-epitxdb.mm.mm10

• bioconductor-celldex

• bioconductor-curatedmetagenomicdata

• bioconductor-genomicstate

• bioconductor-gseabenchmarker

• bioconductor-biscuiteerdata

• bioconductor-circrnaprofiler

• bioconductor-mcsurvdata

• bioconductor-adductomicsr

• bioconductor-tenxbraindata

• bioconductor-pwomics

• bioconductor-alternativesplicingevents.hg38

• bioconductor-phastcons30way.ucsc.hg38

• bioconductor-eupathdb

• bioconductor-psichomics

• bioconductor-tartare

• bioconductor-sctensor

• bioconductor-epitxdb.sc.saccer3

• bioconductor-metaboliteidmapping

• bioconductor-ipddb

• bioconductor-remp

• bioconductor-dmrseq

• bioconductor-hcadata

• bioconductor-curatedtcgadata

• bioconductor-hmp16sdata

• bioconductor-metagxpancreas

• bioconductor-tenxbusdata

• bioconductor-singlecellmultimodal

• bioconductor-chipseqdbdata

• bioconductor-grasp2db

• bioconductor-tsrchitect

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-annotationhub

and update with:

conda update bioconductor-annotationhub

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-annotationhub:<tag>

(see bioconductor-annotationhub/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-annotationhub/README.html)