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Title: Tools for making and manipulating transcript centric annotations
Version: 1.26.2
Encoding: UTF-8
Author: M. Carlson, H. Pagès, P. Aboyoun, S. Falcon, M. Morgan,
D. Sarkar, M. Lawrence
License: Artistic-2.0
Description: 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.
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.47), IRanges (>=
2.3.21), GenomeInfoDb (>= 1.5.16), GenomicRanges (>= 1.21.32),
AnnotationDbi (>= 1.33.15)
Imports: methods, utils, stats, tools, DBI, RSQLite, RCurl, XVector,
Biostrings (>= 2.23.3), rtracklayer (>= 1.29.24), biomaRt (>=
2.17.1), Biobase (>= 2.15.1)
Suggests: 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
Collate: 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 mapIdsToRanges.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 zzz.R
VignetteBuilder: knitr
biocViews: Genetics, Infrastructure, Annotation, Sequencing,
GenomeAnnotation
NeedsCompilation: no
Packaged: 2016-12-16 23:32:48 UTC; biocbuild
Built: R 3.3.2; ; 'Thu, 05 Jan 2017 16:30:05 +0100'; unix
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