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.
|Author||M. Carlson, H. Pagès, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence|
|Date of publication||None|
|Maintainer||Bioconductor Package Maintainer <email@example.com>|
as-format-methods: Coerce to file format structures
coordinate-mapping-methods: Map range coordinates between transcripts and genome space
coverageByTranscript: Compute coverage by transcript (or CDS) of a set of ranges
DEFAULT_CIRC_SEQS: character vector: strings that are usually circular...
disjointExons: Extract non-overlapping exon parts from an object
extractTranscriptSeqs: Extract transcript (or CDS) sequences from chromosome...
extractUpstreamSeqs: Extract sequences upstream of a set of genes or transcripts
FeatureDb-class: FeatureDb objects
features: Extract simple features from a FeatureDb object
getPromoterSeq-methods: Get gene promoter sequences
id2name: Map internal ids to external names for a given feature type
makeFeatureDbFromUCSC: Making a FeatureDb object from annotations available at the...
makeTxDb: Making a TxDb object from user supplied annotations
makeTxDbFromBiomart: Make a TxDb object from annotations available on a BioMart...
makeTxDbFromGFF: Make a TxDb object from annotations available as a GFF3 or...
makeTxDbFromGRanges: Make a TxDb object from a GRanges object
makeTxDbFromUCSC: Make a TxDb object from annotations available at the UCSC...
makeTxDbPackage: Making a TxDb package from annotations available at the UCSC...
mapIdsToRanges: Map IDs to Genomic Ranges
mapRangesToIds: Map Genomic Ranges to IDs
microRNAs: Extract microRNA or tRNA genomic ranges from an object
nearest-methods: Finding the nearest genomic range neighbor in a TxDb
select-methods: Using the "select" interface on TxDb objects
transcriptLengths: Extract the transcript lengths from a TxDb object
transcriptLocs2refLocs: Converting transcript-based locations into reference-based...
transcripts: Extract genomic features from an object
transcriptsBy: Extract and group genomic features of a given type
transcriptsByOverlaps: Extract genomic features from an object based on their by...
TxDb-class: TxDb objects