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
Version1.26.3

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

Functions

asBED,TxDb-method Man page
asGFF,TxDb-method Man page
as.list,TxDb-method Man page
browseUCSCtrack Man page
cds Man page
cdsBy Man page
cdsByOverlaps Man page
cdsByOverlaps,TxDb-method Man page
cdsBy,TxDb-method Man page
cds,TxDb-method Man page
class:FeatureDb Man page
class:TxDb Man page
columns,TxDb-method Man page
coordinate-mapping Man page
coverageByTranscript Man page
DEFAULT_CIRC_SEQS Man page
disjointExons Man page
disjointExons,TxDb-method Man page
distance,GenomicRanges,TxDb-method Man page
exons Man page
exonsBy Man page
exonsByOverlaps Man page
exonsByOverlaps,TxDb-method Man page
exonsBy,TxDb-method Man page
exons,TxDb-method Man page
extractTranscriptSeqs Man page
extractTranscriptSeqs,ANY-method Man page
extractTranscriptSeqs,DNAString-method Man page
extractUpstreamSeqs Man page
extractUpstreamSeqs,GenomicRanges-method Man page
extractUpstreamSeqs,GRangesList-method Man page
extractUpstreamSeqs,TxDb-method Man page
FeatureDb Man page
FeatureDb-class Man page
features Man page
features,FeatureDb-method Man page
fiveUTRsByTranscript Man page
fiveUTRsByTranscript,TxDb-method Man page
genes Man page
genes,TxDb-method Man page
getChromInfoFromBiomart Man page
getChromInfoFromUCSC Man page
getPromoterSeq Man page
getPromoterSeq,GRangesList-method Man page
getPromoterSeq,GRanges-method Man page
id2name Man page
intronsByTranscript Man page
intronsByTranscript,TxDb-method Man page
isActiveSeq Man page
isActiveSeq<- Man page
isActiveSeq<-,TxDb-method Man page
isActiveSeq,TxDb-method Man page
keys,TxDb-method Man page
keytypes,TxDb-method Man page
makeFDbPackageFromUCSC Man page
makeFeatureDbFromUCSC Man page
makePackageName Man page
makeTxDb Man page
makeTxDbFromBiomart Man page
makeTxDbFromGFF Man page
makeTxDbFromGRanges Man page
makeTxDbFromUCSC Man page
makeTxDbPackage Man page
makeTxDbPackageFromBiomart Man page
makeTxDbPackageFromUCSC Man page
mapFromTranscripts Man page
mapFromTranscripts,GenomicRanges,GenomicRanges-method Man page
mapFromTranscripts,GenomicRanges,GRangesList-method Man page
mapIdsToRanges Man page
mapIdsToRanges,TxDb-method Man page
mapRangesToIds Man page
mapRangesToIds,TxDb-method Man page
mapToTranscripts Man page
mapToTranscripts,ANY,TxDb-method Man page
mapToTranscripts,GenomicRanges,GenomicRanges-method Man page
mapToTranscripts,GenomicRanges,GRangesList-method Man page
microRNAs Man page
microRNAs,TxDb-method Man page
nearest-methods Man page
organism,TxDb-method Man page
pcoverageByTranscript Man page
pmapFromTranscripts Man page
pmapFromTranscripts,GenomicRanges,GenomicRanges-method Man page
pmapFromTranscripts,GenomicRanges,GRangesList-method Man page
pmapFromTranscripts,Ranges,GenomicRanges-method Man page
pmapFromTranscripts,Ranges,GRangesList-method Man page
pmapToTranscripts Man page
pmapToTranscripts,GenomicRanges,GenomicRanges-method Man page
pmapToTranscripts,GenomicRanges,GRangesList-method Man page
pmapToTranscripts,GRangesList,GRangesList-method Man page
promoters Man page
promoters,TxDb-method Man page
select-methods Man page
select,TxDb-method Man page
seqinfo,TxDb-method Man page
seqlevels0,TxDb-method Man page
seqlevels<-,TxDb-method Man page
show,TxDb-method Man page
species,TxDb-method Man page
supportedMiRBaseBuildValues Man page
supportedUCSCFeatureDbTables Man page
supportedUCSCFeatureDbTracks Man page
supportedUCSCtables Man page
threeUTRsByTranscript Man page
threeUTRsByTranscript,TxDb-method Man page
transcriptLengths Man page
transcriptLocs2refLocs Man page
transcripts Man page
transcriptsBy Man page
transcriptsByOverlaps Man page
transcriptsByOverlaps,TxDb-method Man page
transcriptsBy,TxDb-method Man page
transcripts,TxDb-method Man page
transcriptWidths Man page
tRNAs Man page
tRNAs,TxDb-method Man page
TxDb Man page
TxDb-class Man page
UCSCFeatureDbTableSchema Man page

Files

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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