GenomicFeatures
Tools for making and manipulating transcript centric annotations
Bioconductor version: Release (2.12)
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.
Author: M. Carlson, H. Pages, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GenomicFeatures")
To cite this package in a publication, start R and enter:
citation("GenomicFeatures")
Documentation
Details
| biocViews |
Annotation, Genetics, HighThroughputSequencing, Infrastructure, Software |
| Version |
1.12.4 |
| In Bioconductor since |
BioC 2.5 (R-2.10) |
| License |
Artistic-2.0 |
| Depends |
BiocGenerics(>= 0.1.0), IRanges(>= 1.17.13), GenomicRanges(>= 1.11.11), AnnotationDbi(>= 1.19.36) |
| Imports |
methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), BiocGenerics, IRanges, GenomicRanges, Biostrings(>= 2.23.2), rtracklayer(>= 1.15.1), biomaRt, 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), RUnit |
| System Requirements |
|
| URL |
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| Depends On Me |
ChIPpeakAnno, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FDb.UCSC.snp135common.hg19, FDb.UCSC.snp137common.hg19, FDb.UCSC.tRNAs, ggtut, Homo.sapiens, IlluminaHumanMethylation450kprobe, Mus.musculus, OrganismDbi, Rattus.norvegicus, SplicingGraphs, TxDb.Athaliana.BioMart.plantsmart10, TxDb.Athaliana.BioMart.plantsmart12, TxDb.Athaliana.BioMart.plantsmart14, TxDb.Athaliana.BioMart.plantsmart16, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Mmusculus.UCSC.mm10.ensGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Scerevisiae.UCSC.sacCer2.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene |
| Imports Me |
biovizBase, casper, ChIPpeakAnno, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FDb.UCSC.snp135common.hg19, FDb.UCSC.snp137common.hg19, FDb.UCSC.tRNAs, geneLenDataBase, ggbio, gmapR, Gviz, Homo.sapiens, HTSeqGenie, MEDIPS, methyAnalysis, Mus.musculus, QuasR, Rattus.norvegicus, SplicingGraphs, TxDb.Athaliana.BioMart.plantsmart10, TxDb.Athaliana.BioMart.plantsmart12, TxDb.Athaliana.BioMart.plantsmart14, TxDb.Athaliana.BioMart.plantsmart16, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Mmusculus.UCSC.mm10.ensGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Scerevisiae.UCSC.sacCer2.sgdGene, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, VariantAnnotation, VariantTools |
| Suggests Me |
biomvRCNS, Biostrings, chipseq, DEXSeq, easyRNASeq, GenomicRanges, ggtut, Gviz, HTSeqGenie, ind1KG, MiRaGE, RIPSeeker, Rsamtools, ShortRead |
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