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GenomeInfoDb:Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
Maintained by Hervé Pagès. Last updated 2 months ago.
geneticsdatarepresentationannotationgenomeannotationbioconductor-packagecore-package
32 stars 16.32 score 1.3k scripts 1.7k 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
trackViewer:A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.
Maintained by Jianhong Ou. Last updated 5 days ago.
8.68 score 145 scripts 2 dependents