GenomicFeatures: 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.

AuthorM. Carlson, H. Pag├Ęs, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.26.2

View on Bioconductor

Man pages

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

Files in this package

GenomicFeatures/DESCRIPTION
GenomicFeatures/NAMESPACE
GenomicFeatures/NEWS
GenomicFeatures/R
GenomicFeatures/R/Ensembl.utils.R GenomicFeatures/R/FeatureDb-class.R GenomicFeatures/R/TxDb-SELECT-helpers.R GenomicFeatures/R/TxDb-class.R GenomicFeatures/R/coordinate-mapping-methods.R GenomicFeatures/R/coverageByTranscript.R GenomicFeatures/R/disjointExons.R GenomicFeatures/R/extractTranscriptSeqs.R GenomicFeatures/R/extractUpstreamSeqs.R GenomicFeatures/R/features.R GenomicFeatures/R/findCompatibleMarts.R GenomicFeatures/R/getPromoterSeq-methods.R GenomicFeatures/R/id2name.R GenomicFeatures/R/makeFeatureDbFromUCSC.R GenomicFeatures/R/makeTxDb.R GenomicFeatures/R/makeTxDbFromBiomart.R GenomicFeatures/R/makeTxDbFromGFF.R GenomicFeatures/R/makeTxDbFromGRanges.R GenomicFeatures/R/makeTxDbFromUCSC.R GenomicFeatures/R/makeTxDbPackage.R GenomicFeatures/R/mapIdsToRanges.R GenomicFeatures/R/microRNAs.R GenomicFeatures/R/nearest-methods.R GenomicFeatures/R/select-methods.R GenomicFeatures/R/transcriptLengths.R GenomicFeatures/R/transcriptLocs2refLocs.R GenomicFeatures/R/transcripts.R GenomicFeatures/R/transcriptsBy.R GenomicFeatures/R/transcriptsByOverlaps.R GenomicFeatures/R/utils.R GenomicFeatures/R/zzz.R
GenomicFeatures/TODO
GenomicFeatures/build
GenomicFeatures/build/vignette.rds
GenomicFeatures/inst
GenomicFeatures/inst/CITATION
GenomicFeatures/inst/doc
GenomicFeatures/inst/doc/GenomicFeatures.R
GenomicFeatures/inst/doc/GenomicFeatures.Rnw
GenomicFeatures/inst/doc/GenomicFeatures.pdf
GenomicFeatures/inst/extdata
GenomicFeatures/inst/extdata/Biomart_Ensembl_sample.sqlite
GenomicFeatures/inst/extdata/FeatureDb.sqlite
GenomicFeatures/inst/extdata/GFF3_files
GenomicFeatures/inst/extdata/GFF3_files/NC_011025.gff
GenomicFeatures/inst/extdata/GFF3_files/TheCanonicalGene_v1.gff3
GenomicFeatures/inst/extdata/GFF3_files/TheCanonicalGene_v2.gff3
GenomicFeatures/inst/extdata/GFF3_files/a.gff3
GenomicFeatures/inst/extdata/GFF3_files/a.sqlite
GenomicFeatures/inst/extdata/GFF3_files/dmel-1000-r5.11.filtered.gff
GenomicFeatures/inst/extdata/GFF3_files/dmel-1000-r5.11.filtered.sqlite
GenomicFeatures/inst/extdata/GTF_files
GenomicFeatures/inst/extdata/GTF_files/Aedes_aegypti.partial.gtf
GenomicFeatures/inst/extdata/GTF_files/Aedes_aegypti.partial.sqlite
GenomicFeatures/inst/extdata/GTF_files/test1.gtf
GenomicFeatures/inst/extdata/cD.exByEdge-SG-Vig.Rda
GenomicFeatures/inst/extdata/cD.exsByGenes-SG-Vig.Rda
GenomicFeatures/inst/extdata/events.Rda
GenomicFeatures/inst/extdata/hg19_knownGene_sample.rda
GenomicFeatures/inst/extdata/hg19_knownGene_sample.sqlite
GenomicFeatures/inst/extdata/hg19_knownToLocusLink_sample.rda
GenomicFeatures/inst/extdata/sample_ranges.rds
GenomicFeatures/inst/script
GenomicFeatures/inst/script/makeTxDbs.R
GenomicFeatures/inst/script/maketRNAFDb.R
GenomicFeatures/inst/txdb-template
GenomicFeatures/inst/txdb-template/DESCRIPTION
GenomicFeatures/inst/txdb-template/NAMESPACE
GenomicFeatures/inst/txdb-template/R
GenomicFeatures/inst/txdb-template/R/zzz.R
GenomicFeatures/inst/txdb-template/inst
GenomicFeatures/inst/txdb-template/inst/extdata
GenomicFeatures/inst/txdb-template/man
GenomicFeatures/inst/txdb-template/man/package.Rd
GenomicFeatures/inst/unitTests
GenomicFeatures/inst/unitTests/test_TxDb_seqinfo.R
GenomicFeatures/inst/unitTests/test_coordinate-mapping-methods.R
GenomicFeatures/inst/unitTests/test_disjointExons.R
GenomicFeatures/inst/unitTests/test_getPromoterSeq-methods.R
GenomicFeatures/inst/unitTests/test_makeIdsForUniqueDataFrameRows.R
GenomicFeatures/inst/unitTests/test_makeTxDb.R
GenomicFeatures/inst/unitTests/test_makeTxDbFromBiomart.R
GenomicFeatures/inst/unitTests/test_makeTxDbFromGFF.R
GenomicFeatures/inst/unitTests/test_makeTxDbFromGRanges.R
GenomicFeatures/inst/unitTests/test_makeTxDbFromUCSC.R
GenomicFeatures/inst/unitTests/test_mapIdsToRanges.R
GenomicFeatures/inst/unitTests/test_select-methods.R
GenomicFeatures/inst/unitTests/test_transcripts.R
GenomicFeatures/inst/unitTests/test_transcriptsBy.R
GenomicFeatures/inst/unitTests/test_transcriptsByOverlaps.R
GenomicFeatures/man
GenomicFeatures/man/DEFAULT_CIRC_SEQS.Rd GenomicFeatures/man/FeatureDb-class.Rd GenomicFeatures/man/TxDb-class.Rd GenomicFeatures/man/as-format-methods.Rd GenomicFeatures/man/coordinate-mapping-methods.Rd GenomicFeatures/man/coverageByTranscript.Rd GenomicFeatures/man/disjointExons.Rd GenomicFeatures/man/extractTranscriptSeqs.Rd GenomicFeatures/man/extractUpstreamSeqs.Rd GenomicFeatures/man/features.Rd GenomicFeatures/man/getPromoterSeq-methods.Rd GenomicFeatures/man/id2name.Rd GenomicFeatures/man/makeFeatureDbFromUCSC.Rd GenomicFeatures/man/makeTxDb.Rd GenomicFeatures/man/makeTxDbFromBiomart.Rd GenomicFeatures/man/makeTxDbFromGFF.Rd GenomicFeatures/man/makeTxDbFromGRanges.Rd GenomicFeatures/man/makeTxDbFromUCSC.Rd GenomicFeatures/man/makeTxDbPackage.Rd GenomicFeatures/man/mapIdsToRanges.Rd GenomicFeatures/man/mapRangesToIds.Rd GenomicFeatures/man/microRNAs.Rd GenomicFeatures/man/nearest-methods.Rd GenomicFeatures/man/select-methods.Rd GenomicFeatures/man/transcriptLengths.Rd GenomicFeatures/man/transcriptLocs2refLocs.Rd GenomicFeatures/man/transcripts.Rd GenomicFeatures/man/transcriptsBy.Rd GenomicFeatures/man/transcriptsByOverlaps.Rd
GenomicFeatures/tests
GenomicFeatures/tests/run_unitTests.R
GenomicFeatures/vignettes
GenomicFeatures/vignettes/GenomicFeatures.Rnw

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