Tools for making and manipulating transcript centric annotations
M. Carlson, H. Pagès, P. Aboyoun, S. Falcon, M. Morgan,
        D. Sarkar, M. Lawrence
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, tools, DBI (>= 0.2-5), RSQLite (>= 0.8-1),
RCurl, XVector, Biostrings (>= 2.23.3), rtracklayer (>=
1.29.24), biomaRt (>= 2.17.1), Biobase (>= 2.15.1)
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,
TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts,
TxDb.Hsapiens.UCSC.hg38.knownGene,
SNPlocs.Hsapiens.dbSNP141.GRCh38, Rsamtools, pasillaBamSubset
(>= 0.0.5), GenomicAlignments, RUnit, BiocStyle, knitr
utils.R TxDb-SELECT-helpers.R Ensembl.utils.R
findCompatibleMarts.R TxDb-class.R FeatureDb-class.R makeTxDb.R
makeTxDbFromUCSC.R makeTxDbFromBiomart.R makeTxDbFromGRanges.R
makeTxDbFromGFF.R makeFeatureDbFromUCSC.R id2name.R
transcripts.R transcriptsBy.R transcriptsByOverlaps.R
transcriptLengths.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
test_GenomicFeatures_package.R
Genetics, Infrastructure, Annotation, Sequencing,
GenomeAnnotation