Conveniently import and query gene models
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.
Genetics, Infrastructure, Annotation, Sequencing,
GenomeAnnotation
c(
	person("M.", "Carlson", role="aut"),
	person("H.", "Pagès", role=c("aut", "cre"),
		email="hpages.on.github@gmail.com"),
	person("P.", "Aboyoun", role="aut"),
	person("S.", "Falcon", role="aut"),
	person("M.", "Morgan", role="aut"),
	person("D.", "Sarkar", role="aut"),
	person("M.", "Lawrence", role="aut"),
	person("V.", "Obenchain", role="aut"),
	person("S.", "Arora", role="ctb"),
	person("J.", "MacDonald", role="ctb"),
	person("M.", "Ramos", role="ctb"),
	person("S.", "Saini", role="ctb"),
	person("P.", "Shannon", role="ctb"),
	person("L.", "Shepherd", role="ctb"),
	person("D.", "Tenenbaum", role="ctb"),
	person("D.", "Van Twisk", role="ctb"))
methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl,
XVector (>= 0.19.7), Biostrings (>= 2.47.6), BiocIO,
rtracklayer (>= 1.51.5), 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.ce11, BSgenome.Dmelanogaster.UCSC.dm3
(>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Celegans.UCSC.ce11.ensGene,
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,
AnnotationFilter, RUnit, BiocStyle, knitr, markdown
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 extendExonsIntoIntrons.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 proteinToGenome.R
coverageByTranscript.R zzz.R
M. Carlson [aut],
  H. Pagès [aut, cre],
  P. Aboyoun [aut],
  S. Falcon [aut],
  M. Morgan [aut],
  D. Sarkar [aut],
  M. Lawrence [aut],
  V. Obenchain [aut],
  S. Arora [ctb],
  J. MacDonald [ctb],
  M. Ramos [ctb],
  S. Saini [ctb],
  P. Shannon [ctb],
  L. Shepherd [ctb],
  D. Tenenbaum [ctb],
  D. Van Twisk [ctb]