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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | Package: GenomicFeatures
Title: Tools for making and manipulating transcript centric annotations
Version: 1.14.2
Author: M. Carlson, H. Pages, 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), IRanges (>= 1.17.13), GenomicRanges
(>= 1.13.16), AnnotationDbi (>= 1.23.14)
Imports: methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), BiocGenerics,
IRanges, GenomicRanges, Biostrings (>= 2.23.2), rtracklayer (>=
1.15.1), biomaRt (>= 2.17.1), RCurl, utils, Biobase (>= 2.15.1)
Suggests: rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, BSgenome,
BSgenome.Hsapiens.UCSC.hg18 (>= 1.3.14),
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.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), Rsamtools,
pasillaBamSubset (>= 0.0.5), seqnames.db, RUnit
Collate: utils.R Ensembl.utils.R TranscriptDb-class.R FeatureDb-class.R
makeTranscriptDb.R makeTranscriptDbFromUCSC.R
makeTranscriptDbFromBiomart.R makeTranscriptDbFromGFF.R
makeFeatureDbFromUCSC.R saveFeatures.R id2name.R transcripts.R
transcriptsByOverlaps.R transcriptsBy.R regions.R features.R
extractTranscriptsFromGenome.R makeTxDbPackage.R
seqnames-methods.R select-methods.R nearest-methods.R
getPromoterSeq-methods.R test_GenomicFeatures_package.R
biocViews: Genetics, Infrastructure, Annotation,
HighThroughputSequencing
Packaged: 2013-11-18 04:54:28 UTC; biocbuild
Built: R 3.0.2; ; 2013-12-29 11:11:38 UTC; unix
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