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Package: AnnotationHubData
Type: Package
Title: Transform public data resources into Bioconductor Data
Structures
Version: 1.2.2
Authors@R:
c(person("Martin", "Morgan", role="ctb"),
person("Marc", "Carlson", role="ctb"),
person("Dan", "Tenenbaum", role="ctb"),
person("Sonali", "Arora", role="ctb"),
person("Paul", "Shannon", role="ctb"),
person("Bioconductor Package Maintainer",
email="maintainer@bioconductor.org", role="cre"))
Depends: R (>= 3.2.2), methods , S4Vectors (>= 0.7.21), IRanges (>=
2.3.23), GenomicRanges , AnnotationHub
Suggests: RUnit , knitr , RMySQL , BiocStyle , grasp2db
Imports: GenomicFeatures , Rsamtools , rtracklayer , BiocGenerics ,
jsonlite , BiocInstaller , httr , AnnotationDbi , Biobase ,
Biostrings , DBI , GEOquery , GenomeInfoDb , OrganismDbi , RSQLite ,
rBiopaxParser , AnnotationForge , futile.logger (>= 1.3.0), XML ,
xml2 , curl
Description: These recipes convert a wide variety and a growing number of
public bioinformatic data sets into easily-used standard Bioconductor data
structures.
License: Artistic-2.0
LazyLoad: yes
biocViews: DataImport
VignetteBuilder: knitr
Collate: Message-class.R ImportPreparer-class.R
makeAnnotationHubResource.R HubMetadata-class.R
AnnotationHubMetadata-class.R utils.R updateResources.R
ahmToJson.R webAccessFunctions.R makeBioPaxImporter.R
makeChEA.R makedbSNPVCF.R makeEncodeDCC.R
makeEnsemblGtfToGRanges.R makeEnsemblFasta.R
makeEpigenomeRoadmap.R makeGencodeFasta.R makeGenecodeGFF.R
makeGrasp2Db.R makeGSE62944ToExpressionSet.R makeHaemCode.R
makeInparanoid8ToDbs.R makeNCBIToOrgDbs.R
makeRecentOrgPkgsToDbs.R makePazar.R makeRefNet.R
makeUCSCChain.R makeUCSC2Bit.R makeUCSCTracks.R
trackWithAuxiliaryTableToGRangesRecipe.R
UCSCTrackUpdateChecker.R makeEnsemblTwoBit.R
NeedsCompilation: no
Packaged: 2016-05-16 05:39:14 UTC; biocbuild
Author: Martin Morgan [ctb],
Marc Carlson [ctb],
Dan Tenenbaum [ctb],
Sonali Arora [ctb],
Paul Shannon [ctb],
Bioconductor Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Package: RefNet
Type: Package
Title: A queryable collection of molecular interactions, from many
sources
Version: 1.8.0
Date: 2016-01-27
Author: Paul Shannon
Maintainer: Paul Shannon <pshannon@systemsbiology.org>
Depends: R (>= 2.15.0), methods , IRanges , PSICQUIC , AnnotationHub ,
RCurl , shiny
Suggests: RUnit , BiocStyle , org.Hs.eg.db
Imports: BiocGenerics
Description: Molecular interactions with metadata, some archived, some
dynamically obtained
License: Artistic-2.0
LazyLoad: yes
biocViews: GraphAndNetwork
Packaged: 2016-05-05 04:23:15 UTC; biocbuild
NeedsCompilation: no
● Data Source:
BioConductor
● BiocViews: GraphAndNetwork
●
0 images,
7 functions ,
0 datasets
●
Reverse Depends: 0
Package: ProteomicsAnnotationHubData
Title: Transform public proteomics data resources into Bioconductor
Data Structures
Version: 1.2.2
Authors@R: c(person("Gatto", "Laurent", role=c("aut", "cre"),
email = "lg390@cam.ac.uk"),
person("Sonali", "Arora", role="aut"))
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
Description: These recipes convert a variety and a growing number of
public proteomics data sets into easily-used standard
Bioconductor data structures.
Depends: AnnotationHub (>= 2.1.45), AnnotationHubData ,
Imports: mzR (>= 2.3.2), MSnbase , Biostrings , GenomeInfoDb , utils ,
Biobase , BiocInstaller , RCurl
Suggests: knitr , BiocStyle , rmarkdown , testthat
biocViews: DataImport, Proteomics
VignetteBuilder: knitr
License: Artistic-2.0
URL: https://github.com/lgatto/ProteomicsAnnotationHubData
BugReports:
https://github.com/lgatto/ProteomicsAnnotationHubData/issues
Collate: ProteomicsAnnotationHubData.R utils.R PAHD.R zzz.R
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 05:40:00 UTC; biocbuild
Author: Gatto Laurent [aut, cre],
Sonali Arora [aut]
● Data Source:
BioConductor
● BiocViews: DataImport, Proteomics
●
0 images,
6 functions ,
1 datasets
●
Reverse Depends: 0
Package: ExperimentHubData
Type: Package
Title: Add resources to ExperimentHub
Version: 0.99.11
Authors@R:
c(person("Bioconductor", "Maintainer",
email="maintainer@bioconductor.org", role="cre"))
biocViews: Infrastructure, DataImport, GUI, ThirdPartyClient
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Description: Functions to add metadata to ExperimentHub db and
resource files to AWS S3 buckets.
License: Artistic-2.0
Depends: BiocGenerics (>= 0.15.10), S4Vectors , AnnotationHubData (>=
1.1.4), AnnotationHub
Imports: methods , BiocInstaller , httr , curl
Suggests: GenomeInfoDb , RUnit , knitr , BiocStyle
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-02-29 06:49:41 UTC; biocbuild
Author: Bioconductor Maintainer [cre]
● Data Source:
BioConductor
● BiocViews: DataImport, GUI, Infrastructure, ThirdPartyClient
●
0 images,
3 functions ,
0 datasets
●
Reverse Depends: 0
Package: ExperimentHub
Type: Package
Title: Client to access ExperimentHub resources
Version: 0.99.9
Author: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Description: This package provides a client for the Bioconductor
ExperimentHub web resource. ExperimentHub provides a central location
where curated data from experiments, publications or training courses
can be accessed. Each resource has associated metadata, tags and date
of modification. The client creates and manages a local cache of files
retrieved enabling quick and reproducible access.
License: Artistic-2.0
biocViews: Infrastructure, DataImport, GUI, ThirdPartyClient
Depends: methods , BiocGenerics (>= 0.15.10), AnnotationHub (>= 2.3.17)
Imports: utils , S4Vectors , BiocInstaller
Suggests: knitr , BiocStyle
Enhances: ExperimentHubData
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-04-19 08:33:18 UTC; biocbuild
● Data Source:
BioConductor
● BiocViews: DataImport, GUI, Infrastructure, ThirdPartyClient
●
0 images,
2 functions ,
0 datasets
●
Reverse Depends: 0