GenomicFeatures v1.24.4

Tools for making and manipulating transcript centric annotations

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.

Functions in GenomicFeatures

Name Description
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
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Encoding UTF-8
License Artistic-2.0
Collate utils.R TxDb-SELECT-helpers.R Ensembl.utils.R findCompatibleMarts.R TxDb-class.R FeatureDb-class.R makeTxDb.R makeTxDbFromUCSC.R makeTxDbFromBiomart.R makeTxDbFromGRanges.R makeTxDbFromGFF.R makeFeatureDbFromUCSC.R mapIdsToRanges.R id2name.R transcripts.R transcriptsBy.R transcriptsByOverlaps.R transcriptLengths.R disjointExons.R features.R microRNAs.R extractTranscriptSeqs.R extractUpstreamSeqs.R getPromoterSeq-methods.R makeTxDbPackage.R select-methods.R nearest-methods.R transcriptLocs2refLocs.R coordinate-mapping-methods.R coverageByTranscript.R zzz.R
VignetteBuilder knitr
biocViews Genetics, Infrastructure, Annotation, Sequencing, GenomeAnnotation

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