GenomicFeatures: Tools for making and manipulating transcript centric annotations

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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. Pag├Ęs, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.26.0

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