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EnsDb specifications

Information


Unique identifier OMICS_33225
Name EnsDb
Alternative name Ensembldb
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.7.4
Stability Stable
Requirements
BiocGenerics, GenomicRanges, GenomicFeatures, AnnotationFilter
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Laurent Gatto
  • person_outline Johannes Rainer

Additional information


https://bioconductor.org/packages/release/bioc/html/ensembldb.html

EnsDb citations

 (7)
library_books

A cross package Bioconductor workflow for analysing methylation array data

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

[…] .3.1 ## [32] gtable_0.2.0 ## [33] doRNG_1.6 ## [34] Rcpp_0.12.9 ## [35] multtest_2.30.0 ## [36] preprocessCore_1.36.0 ## [37] nlme_3.1-131 ## [38] rtracklayer_1.34.2 ## [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] zlib […]

library_books

Ensembl comparative genomics resources

2016
PMCID: 4761110
PMID: 26896847
DOI: 10.1093/database/bav096

[…] In addition to the web interface, the comparative genomics data in Ensembl are accessible through our public MySQL database server (ensembldb.ensembl.org), via direct download from our FTP site (ftp://ftp.ensembl.org) or using our Perl API (http://www.ensembl.org/info/docs/api/compara/index.html), which includes a variety of examp […]

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

[…] 0.8-66 ## [35] graph_1.48.0 BiocInstaller_1.20.1 ## [37] tools_3.2.2 formatR_1.2.1 ## [39] matrixStats_0.50.1 stringr_1.0.0 ## [41] munsell_0.4.2 cluster_2.0.3 ## [43] ensembldb_1.2.1 lambda.r_1.1.7 ## [45] RCurl_1.95-4.7 dichromat_2.0-0 ## [47] VariantAnnotation_1.16.4 bitops_1.0-6 ## [49] gtable_0.1.2 multtest_2.26.0 ## [51] […]

library_books

Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework

2014
J Proteome Res
PMCID: 4261978
PMID: 25301683
DOI: 10.1021/pr500812t

[…] EnSEMBL cDNA database (version GRCh37.72; 192 628 cDNA sequences; http://z.umn.edu/ensembldb) was downloaded and converted into a three-frame translated cDNA database (5 459 808 protein sequences; http://z.umn.edu/getorfensembl) using getORF, a tool from the EMBOSS suite of software […]

library_books

The Vertebrate Genome Annotation browser 10 years on

2013
Nucleic Acids Res
PMCID: 3964964
PMID: 24316575
DOI: 10.1093/nar/gkt1241

[…] e generally limited to FASTA sequence files, other data can be provided on request. Third, for the species incorporated into Ensembl, the databases are available on the public Ensembl MySQL database (ensembldb.ensembl.org) or can be downloaded from the Ensembl FTP site (ftp://ftp.ensembl.org/pub/current_mysql/). […]

library_books

Protein Subcellular Relocalization Increases the Retention of Eukaryotic Duplicate Genes

2013
Genome Biol Evol
PMCID: 3879971
PMID: 24265504
DOI: 10.1093/gbe/evt183

[…] s were used to obtain the complete set of CDSs for each species. Metazoan coding sequences (CDS) from Ensembl genes were obtained using the following SQL query from the public Ensembl MySQL server at ensembldb.ensembl.org, where ID was a variable interpolated by an ad hoc Perl script that repeated the query once for each species’ database. SELECT m.stable_id,m.description,scds.sequence_cds FROM se […]

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