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AnnotationHub specifications

Information


Unique identifier OMICS_29380
Name AnnotationHub
Restrictions to use None
Community driven No
Data access Application programming interface
User data submission Not allowed
Version 2.12.1
Requirements
methods, IRanges, GenomicRanges, Rsamtools, utils, S4Vectors, GenomeInfoDb, Biostrings, rtracklayer, BiocStyle, grDevices, SummarizedExperiment, RUnit, GenomicFeatures, knitr, BiocInstaller, RSQLite, VariantAnnotation, httr, MSnbase, mzR, yaml, gdsfmt, rBiopaxParser, AnnotationForge, ExperimentHub, curl, BiocGenerics(>=0.15.10), AnnotationDbi(>=1.31.19), interactiveDisplayBase
Maintained No

Documentation


Additional information


https://bioconductor.org/packages/release/bioc/vignettes/AnnotationHub/inst/doc/AnnotationHub.html

AnnotationHub citations

 (5)
library_books

Prediction of genome wide DNA methylation in repetitive elements

2017
Nucleic Acids Res
PMCID: 5587781
PMID: 28911103
DOI: 10.1093/nar/gkx587

[…] bases () to identify and annotate candidate RE loci for methylation prediction. We obtained the RepeatMasker Library (build hg19) and RefSeqGene annotation database (build hg19) through the R package AnnotationHub () (record number AH5122 and AH5040, respectively).Second, for algorithm development and validation, we used data on HapMap (The International HapMap Project) lymphoblastoid cell line (L […]

library_books

A cross package Bioconductor workflow for analysing methylation array data

2017
F1000Res
PMCID: 4916993
PMID: 27347385
DOI: 10.5256/f1000research.9514.r14245

[…] .34.2 ## [39] mime_0.5 ## [40] ensembldb_1.6.2 ## [41] rngtools_1.2.4 ## [42] gtools_3.5.0 ## [43] statmod_1.4.29 ## [44] XML_3.98-1.5 ## [45] beanplot_1.2 ## [46] org.Hs.eg.db_3.4.0 ## [47] AnnotationHub_2.6.5 ## [48] zlibbioc_1.20.0 ## [49] MASS_7.3-45 ## [50] scales_0.4.1 ## [51] BSgenome_1.42.0 ## [52] VariantAnnotation_1.20.3 ## [53] BiocInstaller_1.24.0 ## [54] GEOquery_2.40. […]

library_books

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

2016
F1000Res
PMCID: 5302158
PMID: 28232861
DOI: 10.5256/f1000research.9601.r14695

[…] t _ 0.9–0 25 [8] XML _ 3.98–1.4 26 [9] MotIV _ 1.28.0 27 [10] pathview _ 1.12.0 28 [11] biomaRt _ 2.28.0 29 [12] minet _ 3.30.0 30 [13] clusterProfiler _ 3.0.4 31 [14] DOSE _ 2.10.7 32 [15] AnnotationHub _ 2.4.2 33 [16] ChIPseeker _ 1.8.7 34 [17] ELMER _ 1.4.2 35 [18] ELMER. data_ 1.2.2 36 [19] Homo.sapiens _ 1.3.1 37 [20] TxDb.Hsapiens.UCSC.hg19.knownGene _ 3.2.2 38 [21] org.Hs.eg […]

library_books

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP seq data

2016
F1000Res
PMCID: 4706055
PMID: 26834993
DOI: 10.5256/f1000research.7553.r10876

[…] ctors_0.8.5 ## [26] BiocGenerics_0.16.1 ## [27] Rsubread_1.20.2 ## [28] knitr_1.11 ## [29] BiocStyle_1.8.0 ## ## loaded via a namespace (and not attached): ## [1] httr_1.0.0 regioneR_1.2.0 ## [3] AnnotationHub_2.2.2 splines_3.2.2 ## [5] Formula_1.2-1 shiny_0.12.2 ## [7] interactiveDisplayBase_1.8.0 latticeExtra_0.6-26 ## [9] RBGL_1.46.0 BSgenome_1.38.0 ## [11] lattice_0.20-33 […]

library_books

Public data and open source tools for multi assay genomic investigation of disease

2015
Brief Bioinform
PMCID: 4945830
PMID: 26463000
DOI: 10.1093/bib/bbv080

[…] ave been summarized (http://genomicsclass.github.io/book/pages/annoCheat.html). Recently, major annotation resources from ENCODE and the UCSC Genome Browser are redistributed within Bioconductor via ‘AnnotationHub'.We classify data integration methodologies under three categories: exploratory data analysis, network analysis and supervised meta-analysis. Exploratory data analysis enables one to ide […]

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