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GenomicFeatures:Query the gene models of a given organism/assembly
Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.
Maintained by H. Pagès. Last updated 5 months ago.
geneticsinfrastructureannotationsequencinggenomeannotationbioconductor-packagecore-package
26 stars 15.34 score 5.3k scripts 339 dependentsbioc
ensembldb:Utilities to create and use Ensembl-based annotation databases
The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.
Maintained by Johannes Rainer. Last updated 5 months ago.
geneticsannotationdatasequencingcoverageannotationbioconductorbioconductor-packagesensembl
35 stars 14.08 score 892 scripts 108 dependentsbioc
OrganismDbi:Software to enable the smooth interfacing of different database packages
The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
7.26 score 34 scripts 34 dependentsbioc
Organism.dplyr:dplyr-based Access to Bioconductor Annotation Resources
This package provides an alternative interface to Bioconductor 'annotation' resources, in particular the gene identifier mapping functionality of the 'org' packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the 'TxDb' packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).
Maintained by Martin Morgan. Last updated 12 days ago.
annotationsequencinggenomeannotationbioconductor-packagecore-package
3 stars 6.90 score 63 scripts 1 dependents