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GenomicFeatures (version 1.22.0)

Tools for making and manipulating transcript centric annotations

Description

A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

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Version

Version

1.22.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in GenomicFeatures (1.22.0)

makeTxDbFromUCSC

Make a TxDb object from annotations available at the UCSC Genome Browser

Extract simple features from a FeatureDb object

makeTxDbFromGFF

Make a TxDb object from annotations available as a GFF3 or GTF file

Get gene promoter sequences

makeTxDbFromGRanges

Make a TxDb object from a GRanges object

makeTxDbPackage

Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.

Using the "select" interface on TxDb objects

transcriptLengths

Extract the transcript lengths from a TxDb object

extractUpstreamSeqs

Extract sequences upstream of a set of genes or transcripts

FeatureDb-class

FeatureDb objects

transcriptLocs2refLocs

Converting transcript-based locations into reference-based locations

nearest-methods

Finding the nearest genomic range neighbor in a TxDb

Extract microRNA or tRNA genomic ranges from an object

Extract genomic features from an object

mapToTranscripts

Map range coordinates between transcripts and genome space

as-format-methods

Coerce to file format structures

Extract non-overlapping exon parts from an object

extractTranscriptSeqs

Extract transcript (or CDS) sequences from chromosome sequences

makeTxDbFromBiomart

Make a TxDb object from annotations available on a BioMart database

Making a TxDb object from user supplied annotations

coverageByTranscript

Compute coverage by transcript (or CDS) of a set of ranges

Map internal ids to external names for a given feature type

DEFAULT_CIRC_SEQS

character vector: strings that are usually circular chromosomes

makeFeatureDbFromUCSC

Making a FeatureDb object from annotations available at the UCSC Genome Browser

Extract and group genomic features of a given type

transcriptsByOverlaps

Extract genomic features from an object based on their by genomic location