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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GenomeInfoDb")
In most cases, you don't need to download the package archive at all.
GenomeInfoDb
Utilities for manipulating chromosome and other 'seqname' identifiers
Bioconductor version: 2.14
The Seqnames package contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
Author: Sonali Arora, Martin Morgan, Marc Carlson, H. Pages
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Citation (from within R,
enter citation("GenomeInfoDb")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GenomeInfoDb")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GenomeInfoDb")
| R Script | GenomeInfoDb :Introduction to GenomeInfoDb | |
| GenomeInfoDb: Submitting your organism to GenomeInfoDb | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, DataRepresentation, Genetics, Software |
| Version | 1.0.2 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | Artistic-2.0 |
| Depends | R (>= 3.1) |
| Imports | |
| Suggests | BiocGenerics, IRanges, BSgenome, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr |
| System Requirements | |
| URL | |
| Depends On Me | AnnotationDbi, GenomicRanges, Rsamtools |
| Imports Me | GenomicFeatures, SomaticSignatures, VariantTools |
| Suggests Me | BSgenome, QDNAseq |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GenomeInfoDb_1.0.2.tar.gz |
| Windows Binary | GenomeInfoDb_1.0.2.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | GenomeInfoDb_1.0.2.tgz |
| Mac OS X 10.9 (Mavericks) | GenomeInfoDb_1.0.2.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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