Conveniently import and query gene models
M. Carlson, H. Pagès, P. Aboyoun, S. Falcon, M. Morgan,
	D. Sarkar, M. Lawrence, V. Obenchain
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.
methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl,
XVector (>= 0.19.7), Biostrings (>= 2.47.6), rtracklayer (>=
1.39.7), biomaRt (>= 2.17.1), Biobase (>= 2.15.1)
RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome,
BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17),
BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>=
1.3.17), mirbase.db, FDb.UCSC.tRNAs,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1),
TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7),
TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts,
TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6),
SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset
(>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit,
BiocStyle, knitr
utils.R TxDb-schema.R TxDb-SELECT-helpers.R UCSC-utils.R
Ensembl-utils.R findCompatibleMarts.R TxDb-class.R
FeatureDb-class.R makeTxDb.R makeTxDbFromUCSC.R
makeTxDbFromBiomart.R makeTxDbFromEnsembl.R
makeTxDbFromGRanges.R makeTxDbFromGFF.R makeFeatureDbFromUCSC.R
mapIdsToRanges.R id2name.R transcripts.R transcriptsBy.R
transcriptsByOverlaps.R transcriptLengths.R exonicParts.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
Genetics, Infrastructure, Annotation, Sequencing,
GenomeAnnotation