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GenomicFeatures (version 1.24.4)

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

1.24.4

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in GenomicFeatures (1.24.4)

getPromoterSeq

Get gene promoter sequences
microRNAs

Extract microRNA or tRNA genomic ranges from an object
nearest-methods

Finding the nearest genomic range neighbor in a TxDb
features

Extract simple features from a FeatureDb object
extractUpstreamSeqs

Extract sequences upstream of a set of genes or transcripts
makeTxDb

Making a TxDb object from user supplied annotations
FeatureDb-class

FeatureDb objects
TxDb-class

TxDb objects
makeTxDbFromBiomart

Make a TxDb object from annotations available on a BioMart database
as-format-methods

Coerce to file format structures
mapToTranscripts

Map range coordinates between transcripts and genome space
mapIdsToRanges

Map IDs to Genomic Ranges
transcriptLocs2refLocs

Converting transcript-based locations into reference-based locations
transcripts

Extract genomic features from an object
mapRangesToIds

Map Genomic Ranges to IDs
disjointExons

Extract non-overlapping exon parts from an object
extractTranscriptSeqs

Extract transcript (or CDS) sequences from chromosome sequences
id2name

Map internal ids to external names for a given feature type
select-methods

Using the "select" interface on TxDb objects
makeFeatureDbFromUCSC

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

Extract the transcript lengths from a TxDb object
makeTxDbFromUCSC

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

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

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

character vector: strings that are usually circular chromosomes
makeTxDbFromGFF

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

Make a TxDb object from a GRanges object
transcriptsBy

Extract and group genomic features of a given type
transcriptsByOverlaps

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