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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("Genominator")
In most cases, you don't need to download the package archive at all.
Genominator
Analyze, manage and store genomic data
Bioconductor version: 3.0
Tools for storing, accessing, analyzing and visualizing genomic data.
Author: James Bullard, Kasper Daniel Hansen
Maintainer: James Bullard <bullard at stat.berkeley.edu>
Citation (from within R,
enter citation("Genominator")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("Genominator")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Genominator")
| R Script | Plotting with Genominator | |
| R Script | The Genominator User Guide | |
| R Script | Working with the ShortRead Package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Infrastructure, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), methods, RSQLite, DBI (>= 0.2-5), BiocGenerics(>= 0.1.0), IRanges, GenomeGraphs |
| Imports | graphics, stats, utils |
| LinkingTo | |
| Suggests | biomaRt, ShortRead, yeastRNASeq |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | oneChannelGUI |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | Genominator_1.20.0.tar.gz |
| Windows Binary | Genominator_1.20.0.zip |
| Mac OS X 10.6 (Snow Leopard) | Genominator_1.20.0.tgz |
| Mac OS X 10.9 (Mavericks) | Genominator_1.20.0.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
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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